{ "catalog": { "catalog_id": "2acdd821cb79c4bc", "catalog_version": "14", "schema_version": "0.0.16", "builder_version": "1.4.0", "built_utc": "2026-11-02T04:22:15+00:00", "instance": "aging", "base_url": "https://trishorts.github.io/aging-pipeline/" }, "datasets_are": "One entry per dataset. Each names its page and its full JSON (`json`), which holds every fact on the page including all findings and modifications. `findings_by_severity` and `finding_codes` say what is recorded against a dataset; whether that makes it usable for a question is the question's call, not this file's. `organisms` is the organism of the protein DATABASE the search used, not a statement about the samples. Sample annotation, where any exists, is in the catalog's `samples` and `sample_characteristics` tables.", "datasets": [ { "dataset_id": "PXD001054", "title": "Redox Proteome of Skeletal Muscle", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 9, "n_samples": 9, "n_psms_1pct": 55829, "n_peptidoforms_1pct": 8164, "n_protein_groups_1pct": 912, "n_ptm_sites": 4450, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 1 }, "finding_codes": [ "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD001054 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 55,829 PSMs, 8,164 peptidoforms and 912 protein groups, and the repository holds 4,450 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD001054.html", "json": "datasets/PXD001054.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD001054.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD001054.json" }, { "dataset_id": "PXD002467", "title": "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 96, "n_samples": 48, "n_psms_1pct": 1453769, "n_peptidoforms_1pct": 44050, "n_protein_groups_1pct": 6747, "n_ptm_sites": 29726, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD002467 is a DDA label-free dataset (Rattus norvegicus) with 96 runs, 48 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,453,769 PSMs, 44,050 peptidoforms and 6,747 protein groups, and the repository holds 29,726 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD002467.html", "json": "datasets/PXD002467.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD002467.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD002467.json" }, { "dataset_id": "PXD004916", "title": "Spermidine treated mouse Heart LC-MS/MS", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 54, "n_samples": 54, "n_psms_1pct": 227597, "n_peptidoforms_1pct": 16301, "n_protein_groups_1pct": 2001, "n_ptm_sites": 5536, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 8, "info": 1 }, "finding_codes": [ "contaminant_label_unresolved", "cysteine_poor", "high_contamination", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites", "upstream_provenance_changed" ], "summary": "PXD004916 is a DDA label-free dataset (Mus musculus) with 54 runs, 54 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 227,597 PSMs, 16,301 peptidoforms and 2,001 protein groups, and the repository holds 5,536 PTM sites for it. 8 open warnings about it are recorded.", "page": "datasets/PXD004916.html", "json": "datasets/PXD004916.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD004916.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD004916.json" }, { "dataset_id": "PXD005014", "title": "Proteome of Young and Old Murine Diaphragm and Associaated Changes in Contractile Properties", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 115772, "n_peptidoforms_1pct": 11015, "n_protein_groups_1pct": 1368, "n_ptm_sites": 4483, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 1 }, "finding_codes": [ "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD005014 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 115,772 PSMs, 11,015 peptidoforms and 1,368 protein groups, and the repository holds 4,483 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD005014.html", "json": "datasets/PXD005014.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD005014.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD005014.json" }, { "dataset_id": "PXD005123", "title": "Somatic increase of CCT8 mimics proteostasis of human pluripotent stem cells and extends C. elegans lifespan", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 1101243, "n_peptidoforms_1pct": 86630, "n_protein_groups_1pct": 7889, "n_ptm_sites": 25195, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "unplaced_ptm_sites" ], "summary": "PXD005123 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 1,101,243 PSMs, 86,630 peptidoforms and 7,889 protein groups, and the repository holds 25,195 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD005123.html", "json": "datasets/PXD005123.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD005123.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD005123.json" }, { "dataset_id": "PXD006023", "title": "AGK human LC-MSMS project part I (proteome)", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "other" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 767748, "n_peptidoforms_1pct": 54669, "n_protein_groups_1pct": 5347, "n_ptm_sites": 13244, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "unplaced_ptm_sites" ], "summary": "PXD006023 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and an enrichment step outside the controlled list (recorded as `other`). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 767,748 PSMs, 54,669 peptidoforms and 5,347 protein groups, and the repository holds 13,244 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD006023.html", "json": "datasets/PXD006023.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006023.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006023.json" }, { "dataset_id": "PXD006216", "title": "Chemotherapy-induced cellular senescence is characterized by aberrant lipid regulation and lipid peroxidation", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 30, "n_samples": 30, "n_psms_1pct": 272722, "n_peptidoforms_1pct": 37317, "n_protein_groups_1pct": 3979, "n_ptm_sites": 18744, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD006216 is a DDA label-free dataset (Mus musculus) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 272,722 PSMs, 37,317 peptidoforms and 3,979 protein groups, and the repository holds 18,744 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD006216.html", "json": "datasets/PXD006216.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006216.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006216.json" }, { "dataset_id": "PXD006578", "title": "Aging-related proteome alterations in B cells may predispose for chronic lymphocytic leukemia - cytoplasmic proteins of CLL cells", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 671443, "n_peptidoforms_1pct": 69065, "n_protein_groups_1pct": 6127, "n_ptm_sites": 33985, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "unplaced_ptm_sites" ], "summary": "PXD006578 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 671,443 PSMs, 69,065 peptidoforms and 6,127 protein groups, and the repository holds 33,985 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD006578.html", "json": "datasets/PXD006578.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006578.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006578.json" }, { "dataset_id": "PXD006589", "title": "Aging-related proteome alterations in B cells may predispose for chronic lymphocytic leukemia - nuclear proteins of CLL cells", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 546673, "n_peptidoforms_1pct": 54505, "n_protein_groups_1pct": 5244, "n_ptm_sites": 27252, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "unplaced_ptm_sites" ], "summary": "PXD006589 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 546,673 PSMs, 54,505 peptidoforms and 5,244 protein groups, and the repository holds 27,252 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD006589.html", "json": "datasets/PXD006589.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006589.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006589.json" }, { "dataset_id": "PXD006815", "title": "Changes in glycogen metabolism machinery are associated with brain aging. Proteomic and immunofluorescent evidence for a", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 36, "n_samples": 12, "n_psms_1pct": 1142250, "n_peptidoforms_1pct": 101104, "n_protein_groups_1pct": 7685, "n_ptm_sites": 40002, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "cysteine_poor", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD006815 is a DDA label-free dataset (Mus musculus) with 36 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,142,250 PSMs, 101,104 peptidoforms and 7,685 protein groups, and the repository holds 40,002 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD006815.html", "json": "datasets/PXD006815.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006815.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006815.json" }, { "dataset_id": "PXD006898", "title": "Quantitative proteomics of a human fetal ovary development timecourse", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 618984, "n_peptidoforms_1pct": 61755, "n_protein_groups_1pct": 6520, "n_ptm_sites": 31076, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD006898 is a DDA label-free dataset (Homo sapiens) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 618,984 PSMs, 61,755 peptidoforms and 6,520 protein groups, and the repository holds 31,076 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD006898.html", "json": "datasets/PXD006898.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006898.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD006898.json" }, { "dataset_id": "PXD007035", "title": "Loss-of-function of ubiquitin ligase adaptor LZTR1 triggers human disease by dysregulating RAS ubiquitination", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "ubiquitin_GG" ], "enrichment_mixed": true, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 126015, "n_peptidoforms_1pct": 23955, "n_protein_groups_1pct": 3836, "n_ptm_sites": 9575, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "mixed_enrichment", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD007035 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and runs that differ in enrichment (ubiquitin_GG on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 126,015 PSMs, 23,955 peptidoforms and 3,836 protein groups, and the repository holds 9,575 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD007035.html", "json": "datasets/PXD007035.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD007035.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD007035.json" }, { "dataset_id": "PXD007049", "title": "Loss-of-function of ubiquitin ligase adaptor LZTR1 triggers human disease by dysregulating RAS ubiquitination", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 22417, "n_peptidoforms_1pct": 3745, "n_protein_groups_1pct": 781, "n_ptm_sites": 1827, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD007049 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 22,417 PSMs, 3,745 peptidoforms and 781 protein groups, and the repository holds 1,827 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD007049.html", "json": "datasets/PXD007049.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD007049.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD007049.json" }, { "dataset_id": "PXD007188", "title": "Mevalonate pathway activity is a key determinant of radiation sensitivity in head and neck cancer", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 329746, "n_peptidoforms_1pct": 53692, "n_protein_groups_1pct": 5704, "n_ptm_sites": 27637, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD007188 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 329,746 PSMs, 53,692 peptidoforms and 5,704 protein groups, and the repository holds 27,637 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD007188.html", "json": "datasets/PXD007188.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD007188.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD007188.json" }, { "dataset_id": "PXD007906", "title": "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cell line", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 24, "n_samples": 24, "n_psms_1pct": 882422, "n_peptidoforms_1pct": 41275, "n_protein_groups_1pct": 3487, "n_ptm_sites": 26288, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD007906 is a DDA label-free dataset (Homo sapiens) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 882,422 PSMs, 41,275 peptidoforms and 3,487 protein groups, and the repository holds 26,288 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD007906.html", "json": "datasets/PXD007906.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD007906.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD007906.json" }, { "dataset_id": "PXD007999", "title": "NRF2-dependent ECM - Nrf2-Mediated Fibroblast Reprogramming Drives Cellular Senescence by Targeting the Matrisome", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 30, "n_samples": 30, "n_psms_1pct": 404489, "n_peptidoforms_1pct": 39499, "n_protein_groups_1pct": 4031, "n_ptm_sites": 20858, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 2 }, "finding_codes": [ "contaminant_label_unresolved", "count_mismatch", "high_contamination", "no_design_file", "no_output_sdrf", "no_sdrf", "occupancy_decoy_groups", "unplaced_ptm_sites", "upstream_provenance_changed" ], "summary": "PXD007999 is a DDA label-free dataset (Mus musculus) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 404,489 PSMs, 39,499 peptidoforms and 4,031 protein groups, and the repository holds 20,858 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD007999.html", "json": "datasets/PXD007999.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD007999.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD007999.json" }, { "dataset_id": "PXD008050", "title": "UVA and to UV-oxidized lipids proteomic regulation of the human keratinocytes", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 937570, "n_peptidoforms_1pct": 63990, "n_protein_groups_1pct": 5614, "n_ptm_sites": 40949, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD008050 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 937,570 PSMs, 63,990 peptidoforms and 5,614 protein groups, and the repository holds 40,949 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD008050.html", "json": "datasets/PXD008050.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD008050.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD008050.json" }, { "dataset_id": "PXD008344", "title": "Human brain LC-MS/MS - Brain Citrullination Patterns and T Cell Reactivity of Cerebrospinal Fluid-Derived CD4+ T Cells in Multiple Sclerosis", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 44, "n_samples": 44, "n_psms_1pct": 766417, "n_peptidoforms_1pct": 150696, "n_protein_groups_1pct": 8640, "n_ptm_sites": 61855, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD008344 is a DDA label-free dataset (Homo sapiens) with 44 runs, 44 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 766,417 PSMs, 150,696 peptidoforms and 8,640 protein groups, and the repository holds 61,855 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD008344.html", "json": "datasets/PXD008344.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD008344.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD008344.json" }, { "dataset_id": "PXD008934", "title": "Characterization of proteomic changes in human heart failure", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 34, "n_samples": 34, "n_psms_1pct": 1832742, "n_peptidoforms_1pct": 71950, "n_protein_groups_1pct": 4532, "n_ptm_sites": 66232, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 3, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD008934 is a DDA label-free dataset (Homo sapiens) with 34 runs, 34 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,832,742 PSMs, 71,950 peptidoforms and 4,532 protein groups, and the repository holds 66,232 PTM sites for it. 3 open warnings about it are recorded.", "page": "datasets/PXD008934.html", "json": "datasets/PXD008934.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD008934.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD008934.json" }, { "dataset_id": "PXD008990", "title": "Glycomic and Proteomic changes in aging brain nigrostriatal pathway", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 70, "n_samples": 70, "n_psms_1pct": 534367, "n_peptidoforms_1pct": 11095, "n_protein_groups_1pct": 2195, "n_ptm_sites": 3558, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD008990 is a DDA label-free dataset (Rattus norvegicus) with 70 runs, 70 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 534,367 PSMs, 11,095 peptidoforms and 2,195 protein groups, and the repository holds 3,558 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD008990.html", "json": "datasets/PXD008990.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD008990.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD008990.json" }, { "dataset_id": "PXD009212", "title": "Proteome profiling in aging rat brain by LC-MS/MS", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 57, "n_samples": 57, "n_psms_1pct": 195142, "n_peptidoforms_1pct": 12844, "n_protein_groups_1pct": 1711, "n_ptm_sites": 5753, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "low_id_rate", "mbr_kept_exceeds_msms", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD009212 is a DDA label-free dataset (Rattus norvegicus) with 57 runs, 57 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 195,142 PSMs, 12,844 peptidoforms and 1,711 protein groups, and the repository holds 5,753 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD009212.html", "json": "datasets/PXD009212.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD009212.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD009212.json" }, { "dataset_id": "PXD009430", "title": "Modulation of the ATM / autophagy pathway tips the balance between senescence and apoptosis in response to a quadruplex ligand", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 301057, "n_peptidoforms_1pct": 20480, "n_protein_groups_1pct": 2782, "n_ptm_sites": 16167, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "spectral_library", "unplaced_ptm_sites" ], "summary": "PXD009430 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 301,057 PSMs, 20,480 peptidoforms and 2,782 protein groups, and the repository holds 16,167 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD009430.html", "json": "datasets/PXD009430.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD009430.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD009430.json" }, { "dataset_id": "PXD010091", "title": "miR-181a Restores Mitochondrial Dynamics in Skeletal Muscle Ageing", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 217078, "n_peptidoforms_1pct": 12200, "n_protein_groups_1pct": 1402, "n_ptm_sites": 6526, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD010091 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 217,078 PSMs, 12,200 peptidoforms and 1,402 protein groups, and the repository holds 6,526 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD010091.html", "json": "datasets/PXD010091.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD010091.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD010091.json" }, { "dataset_id": "PXD010115", "title": "Quantification of the Soluble Receptor of Advanced Glycation End-Products (sRAGE) by LC-MS Without the Use of Affinity Enrichment", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 119030, "n_peptidoforms_1pct": 10258, "n_protein_groups_1pct": 445, "n_ptm_sites": 7952, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD010115 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 119,030 PSMs, 10,258 peptidoforms and 445 protein groups, and the repository holds 7,952 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD010115.html", "json": "datasets/PXD010115.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD010115.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD010115.json" }, { "dataset_id": "PXD010820", "title": "O-GlcNAcylation enhances double strand break repair, promotes cancer cell proliferation and prevents therapy-induced senescence in irradiated tumors", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 259817, "n_peptidoforms_1pct": 27693, "n_protein_groups_1pct": 3369, "n_ptm_sites": 16115, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD010820 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 259,817 PSMs, 27,693 peptidoforms and 3,369 protein groups, and the repository holds 16,115 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD010820.html", "json": "datasets/PXD010820.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD010820.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD010820.json" }, { "dataset_id": "PXD011314", "title": "Profiling of Methylglyoxal Blood Metabolism and Advanced Glycation End-Product Proteome using a Chemical Probe", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "chemical_probe" ], "enrichment_mixed": false, "n_runs": 17, "n_samples": 17, "n_psms_1pct": 4868, "n_peptidoforms_1pct": 391, "n_protein_groups_1pct": 57, "n_ptm_sites": 580, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "calibration_failed", "high_contamination", "low_core_use", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD011314 is a DDA label-free dataset (Homo sapiens) with 17 runs, 17 samples and enrichment: chemical_probe. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 4,868 PSMs, 391 peptidoforms and 57 protein groups, and the repository holds 580 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD011314.html", "json": "datasets/PXD011314.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD011314.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD011314.json" }, { "dataset_id": "PXD011740", "title": "Translational regulation contributes to the secretory response of chondrocytic cells following exposure to Interleukin-1B", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 89011, "n_peptidoforms_1pct": 16644, "n_protein_groups_1pct": 2112, "n_ptm_sites": 6207, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites", "unresolved_modifications" ], "summary": "PXD011740 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 89,011 PSMs, 16,644 peptidoforms and 2,112 protein groups, and the repository holds 6,207 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD011740.html", "json": "datasets/PXD011740.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD011740.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD011740.json" }, { "dataset_id": "PXD012213", "title": "Effects of Caloric Restriction with Protein Supplementation on Plasma Protein Profiles in Middle-Aged Women with Metabolic Syndrome – A Preliminary Open Study", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 26, "n_samples": 26, "n_psms_1pct": 193217, "n_peptidoforms_1pct": 4385, "n_protein_groups_1pct": 320, "n_ptm_sites": 4786, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 1 }, "finding_codes": [ "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD012213 is a DDA label-free dataset (Homo sapiens) with 26 runs, 26 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 193,217 PSMs, 4,385 peptidoforms and 320 protein groups, and the repository holds 4,786 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD012213.html", "json": "datasets/PXD012213.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD012213.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD012213.json" }, { "dataset_id": "PXD012307", "title": "An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 32, "n_samples": 1, "n_psms_1pct": 2067679, "n_peptidoforms_1pct": 136878, "n_protein_groups_1pct": 7801, "n_ptm_sites": 95871, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_conflicting_rows", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD012307 is a DDA label-free dataset (Mus musculus) with 32 runs, 1 sample and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 2,067,679 PSMs, 136,878 peptidoforms and 7,801 protein groups, and the repository holds 95,871 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD012307.html", "json": "datasets/PXD012307.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD012307.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD012307.json" }, { "dataset_id": "PXD012753", "title": "Young, old, OVX mouse Skin LC-MSMS, 3M Urea extraction", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 43949, "n_peptidoforms_1pct": 5617, "n_protein_groups_1pct": 1032, "n_ptm_sites": 2912, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "low_id_rate", "mbr_kept_exceeds_msms", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD012753 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 43,949 PSMs, 5,617 peptidoforms and 1,032 protein groups, and the repository holds 2,912 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD012753.html", "json": "datasets/PXD012753.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD012753.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD012753.json" }, { "dataset_id": "PXD012754", "title": "Ageing Mouse Skin LC-MSMS, NaCl extraction", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 10, "n_samples": 10, "n_psms_1pct": 11842, "n_peptidoforms_1pct": 4299, "n_protein_groups_1pct": 780, "n_ptm_sites": 2140, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 8, "info": 0 }, "finding_codes": [ "calibration_failed", "high_contamination", "low_core_use", "low_id_rate", "mbr_kept_exceeds_msms", "no_sdrf", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD012754 is a DDA label-free dataset (Mus musculus) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 11,842 PSMs, 4,299 peptidoforms and 780 protein groups, and the repository holds 2,140 PTM sites for it. 8 open warnings about it are recorded.", "page": "datasets/PXD012754.html", "json": "datasets/PXD012754.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD012754.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD012754.json" }, { "dataset_id": "PXD013240", "title": "Intracellular proteome (SDS/Na-DoC) extract from EP/LP MSCs grown on soft/stiff hydrogels for 4 days", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 16, "n_samples": 16, "n_psms_1pct": 132407, "n_peptidoforms_1pct": 16738, "n_protein_groups_1pct": 2806, "n_ptm_sites": 9315, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 1 }, "finding_codes": [ "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD013240 is a DDA label-free dataset (Homo sapiens) with 16 runs, 16 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 132,407 PSMs, 16,738 peptidoforms and 2,806 protein groups, and the repository holds 9,315 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD013240.html", "json": "datasets/PXD013240.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD013240.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD013240.json" }, { "dataset_id": "PXD013640", "title": "Keap-1-mediated S-nitrosylation of NOX4 hampers oxidative damage in endothelium", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "chemical_probe" ], "enrichment_mixed": false, "n_runs": 16, "n_samples": 16, "n_psms_1pct": 56309, "n_peptidoforms_1pct": 4232, "n_protein_groups_1pct": 793, "n_ptm_sites": 2856, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD013640 is a DDA label-free dataset (Homo sapiens) with 16 runs, 16 samples and enrichment: chemical_probe. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 56,309 PSMs, 4,232 peptidoforms and 793 protein groups, and the repository holds 2,856 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD013640.html", "json": "datasets/PXD013640.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD013640.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD013640.json" }, { "dataset_id": "PXD014097", "title": "Auto-phosphorylation at serine 166 regulates RIP kinase 1 mediated cell death and inflammation", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 150342, "n_peptidoforms_1pct": 20939, "n_protein_groups_1pct": 4072, "n_ptm_sites": 19650, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD014097 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 150,342 PSMs, 20,939 peptidoforms and 4,072 protein groups, and the repository holds 19,650 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD014097.html", "json": "datasets/PXD014097.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD014097.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD014097.json" }, { "dataset_id": "PXD014098", "title": "CLUH-dependent RNA granules coordinate mitochondrial catabolic pathways with mTORC1 signaling and mitophagy", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 16, "n_samples": 16, "n_psms_1pct": 1040626, "n_peptidoforms_1pct": 73647, "n_protein_groups_1pct": 4933, "n_ptm_sites": 32132, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD014098 is a DDA label-free dataset (Mus musculus) with 16 runs, 16 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,040,626 PSMs, 73,647 peptidoforms and 4,933 protein groups, and the repository holds 32,132 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD014098.html", "json": "datasets/PXD014098.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD014098.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD014098.json" }, { "dataset_id": "PXD014274", "title": "Proteomic and unbiased post-translational modification profiling of amyloid plaques and surrounding tissue in a transgenic mouse model of Alzheimer’s disease", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 38, "n_samples": 38, "n_psms_1pct": 116639, "n_peptidoforms_1pct": 6415, "n_protein_groups_1pct": 1318, "n_ptm_sites": 7280, "sdrf_status": "partial", "findings_by_severity": { "error": 0, "warning": 8, "info": 5 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "excluded_from_search", "high_contamination", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_partial", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD014274 is a DDA label-free dataset (Mus musculus) with 38 runs, 38 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 116,639 PSMs, 6,415 peptidoforms and 1,318 protein groups, and the repository holds 7,280 PTM sites for it. 8 open warnings about it are recorded.", "page": "datasets/PXD014274.html", "json": "datasets/PXD014274.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD014274.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD014274.json" }, { "dataset_id": "PXD014416", "title": "Spatiotemporal proteomics of hormone treated mice (urine across time, prostate tissue)", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 47, "n_samples": 47, "n_psms_1pct": 594741, "n_peptidoforms_1pct": 42076, "n_protein_groups_1pct": 4960, "n_ptm_sites": 26873, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD014416 is a DDA label-free dataset (Mus musculus) with 47 runs, 47 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 594,741 PSMs, 42,076 peptidoforms and 4,960 protein groups, and the repository holds 26,873 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD014416.html", "json": "datasets/PXD014416.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD014416.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD014416.json" }, { "dataset_id": "PXD015079", "title": "Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 261188, "n_peptidoforms_1pct": 31951, "n_protein_groups_1pct": 2689, "n_ptm_sites": 11932, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "cysteine_poor", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD015079 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 261,188 PSMs, 31,951 peptidoforms and 2,689 protein groups, and the repository holds 11,932 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD015079.html", "json": "datasets/PXD015079.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD015079.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD015079.json" }, { "dataset_id": "PXD015170", "title": "The GID Ubiquitin Ligase Complex is a Regulator of AMPK Activity and Organismal Lifespan", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 121033, "n_peptidoforms_1pct": 13290, "n_protein_groups_1pct": 2744, "n_ptm_sites": 4189, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD015170 is a DDA label-free dataset (Mus musculus) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 121,033 PSMs, 13,290 peptidoforms and 2,744 protein groups, and the repository holds 4,189 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD015170.html", "json": "datasets/PXD015170.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD015170.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD015170.json" }, { "dataset_id": "PXD015239", "title": "Epigenetic contributions to hemisphere asymmetry in healthy brain, aging, and Parkinson’s disease", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 10, "n_samples": 10, "n_psms_1pct": 229035, "n_peptidoforms_1pct": 21719, "n_protein_groups_1pct": 2140, "n_ptm_sites": 8495, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD015239 is a DDA label-free dataset (Homo sapiens) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 229,035 PSMs, 21,719 peptidoforms and 2,140 protein groups, and the repository holds 8,495 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD015239.html", "json": "datasets/PXD015239.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD015239.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD015239.json" }, { "dataset_id": "PXD015729", "title": "Murine hippocampus after radiation LC-MSMS", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 16, "n_samples": 16, "n_psms_1pct": 319370, "n_peptidoforms_1pct": 25500, "n_protein_groups_1pct": 3051, "n_ptm_sites": 12871, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD015729 is a DDA label-free dataset (Mus musculus) with 16 runs, 16 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 319,370 PSMs, 25,500 peptidoforms and 3,051 protein groups, and the repository holds 12,871 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD015729.html", "json": "datasets/PXD015729.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD015729.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD015729.json" }, { "dataset_id": "PXD016430", "title": "MiR-29 coordinates age-dependent plasticity brakes in the adult visual cortex", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 44, "n_samples": 44, "n_psms_1pct": 759941, "n_peptidoforms_1pct": 20840, "n_protein_groups_1pct": 3715, "n_ptm_sites": 8882, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD016430 is a DDA label-free dataset (Mus musculus) with 44 runs, 44 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 759,941 PSMs, 20,840 peptidoforms and 3,715 protein groups, and the repository holds 8,882 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD016430.html", "json": "datasets/PXD016430.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD016430.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD016430.json" }, { "dataset_id": "PXD016793", "title": "Proteomics analysis of rat liver after disulfiram treatment", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 24, "n_samples": 24, "n_psms_1pct": 2314854, "n_peptidoforms_1pct": 68434, "n_protein_groups_1pct": 5609, "n_ptm_sites": 42538, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "unplaced_ptm_sites" ], "summary": "PXD016793 is a DDA label-free dataset (Rattus norvegicus) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 2,314,854 PSMs, 68,434 peptidoforms and 5,609 protein groups, and the repository holds 42,538 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD016793.html", "json": "datasets/PXD016793.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD016793.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD016793.json" }, { "dataset_id": "PXD017058", "title": "Astrocyte Support for Oligodendrocyte Differentiation can be Conveyed via Extracellular Vesicles but Diminishes with Age", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 9, "n_samples": 9, "n_psms_1pct": 182903, "n_peptidoforms_1pct": 28688, "n_protein_groups_1pct": 2419, "n_ptm_sites": 19068, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD017058 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 182,903 PSMs, 28,688 peptidoforms and 2,419 protein groups, and the repository holds 19,068 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD017058.html", "json": "datasets/PXD017058.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD017058.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD017058.json" }, { "dataset_id": "PXD017475", "title": "The lncRNA MIR31HG regulates the senescence associated secretory phenotype", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 19, "n_samples": 19, "n_psms_1pct": 187253, "n_peptidoforms_1pct": 26410, "n_protein_groups_1pct": 2277, "n_ptm_sites": 17751, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD017475 is a DDA label-free dataset (Homo sapiens) with 19 runs, 19 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 187,253 PSMs, 26,410 peptidoforms and 2,277 protein groups, and the repository holds 17,751 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD017475.html", "json": "datasets/PXD017475.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD017475.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD017475.json" }, { "dataset_id": "PXD017505", "title": "Autofluorescence positive and negative microglia constitute novel subsets found in healthy brain.", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 17, "n_samples": 17, "n_psms_1pct": 522900, "n_peptidoforms_1pct": 21512, "n_protein_groups_1pct": 4078, "n_ptm_sites": 17913, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD017505 is a DDA label-free dataset (Mus musculus) with 17 runs, 17 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 522,900 PSMs, 21,512 peptidoforms and 4,078 protein groups, and the repository holds 17,913 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD017505.html", "json": "datasets/PXD017505.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD017505.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD017505.json" }, { "dataset_id": "PXD017944", "title": "Proteomic analysis of scleraxis mutant tendon", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 69785, "n_peptidoforms_1pct": 9263, "n_protein_groups_1pct": 879, "n_ptm_sites": 5405, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD017944 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 69,785 PSMs, 9,263 peptidoforms and 879 protein groups, and the repository holds 5,405 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD017944.html", "json": "datasets/PXD017944.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD017944.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD017944.json" }, { "dataset_id": "PXD018097", "title": "YME1L1 KnockOut MEF Cells Whole Proteomics", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": true, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 762720, "n_peptidoforms_1pct": 101119, "n_protein_groups_1pct": 8079, "n_ptm_sites": 52657, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "mixed_enrichment", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "spectral_library", "unplaced_ptm_sites" ], "summary": "PXD018097 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and runs that differ in enrichment (phospho on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 762,720 PSMs, 101,119 peptidoforms and 8,079 protein groups, and the repository holds 52,657 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD018097.html", "json": "datasets/PXD018097.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018097.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018097.json" }, { "dataset_id": "PXD018315", "title": "Identification of proteins that interact with the lncRNA Sarrah", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 40, "n_samples": 40, "n_psms_1pct": 79679, "n_peptidoforms_1pct": 7674, "n_protein_groups_1pct": 1442, "n_ptm_sites": 5147, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD018315 is a DDA label-free dataset (Mus musculus) with 40 runs, 40 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 79,679 PSMs, 7,674 peptidoforms and 1,442 protein groups, and the repository holds 5,147 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD018315.html", "json": "datasets/PXD018315.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018315.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018315.json" }, { "dataset_id": "PXD018399", "title": "Reduced proteasome activity in the aging brainresults in ribosome stoichiometry loss and aggregation", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "other" ], "enrichment_mixed": true, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 161098, "n_peptidoforms_1pct": 17155, "n_protein_groups_1pct": 3380, "n_ptm_sites": 5953, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "mixed_enrichment", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD018399 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and runs that differ in enrichment (other on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 161,098 PSMs, 17,155 peptidoforms and 3,380 protein groups, and the repository holds 5,953 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD018399.html", "json": "datasets/PXD018399.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018399.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018399.json" }, { "dataset_id": "PXD018545", "title": "Endoplasmic Reticulum Stress-mediated Mitochondrial Dysfunction in Aged Hearts", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 316110, "n_peptidoforms_1pct": 7742, "n_protein_groups_1pct": 1037, "n_ptm_sites": 7211, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD018545 is a DDA label-free dataset (Mus musculus) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 316,110 PSMs, 7,742 peptidoforms and 1,037 protein groups, and the repository holds 7,211 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD018545.html", "json": "datasets/PXD018545.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018545.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018545.json" }, { "dataset_id": "PXD018655", "title": "Proteomic analysis of small extracellular vesicles derived from human ESCs", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 201398, "n_peptidoforms_1pct": 35524, "n_protein_groups_1pct": 4334, "n_ptm_sites": 16354, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD018655 is a DDA label-free dataset (Homo sapiens) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 201,398 PSMs, 35,524 peptidoforms and 4,334 protein groups, and the repository holds 16,354 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD018655.html", "json": "datasets/PXD018655.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018655.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018655.json" }, { "dataset_id": "PXD018969", "title": "Keap1 governs ageing-induced protein aggregation in endothelial cells", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 19, "n_samples": 19, "n_psms_1pct": 220119, "n_peptidoforms_1pct": 17592, "n_protein_groups_1pct": 2966, "n_ptm_sites": 4903, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 3 }, "finding_codes": [ "collapsed_duplicate_rows", "contaminant_label_unresolved", "count_mismatch", "high_contamination", "no_design_file", "no_output_sdrf", "no_sdrf", "occupancy_decoy_groups", "unplaced_ptm_sites", "upstream_provenance_changed" ], "summary": "PXD018969 is a DDA label-free dataset (Homo sapiens) with 19 runs, 19 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 220,119 PSMs, 17,592 peptidoforms and 2,966 protein groups, and the repository holds 4,903 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD018969.html", "json": "datasets/PXD018969.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018969.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018969.json" }, { "dataset_id": "PXD018999", "title": "A dichotomous response to chronic fetal hypoxia preprograms aging already during kidney development", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 48, "n_samples": 48, "n_psms_1pct": 974746, "n_peptidoforms_1pct": 78290, "n_protein_groups_1pct": 8239, "n_ptm_sites": 46440, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 8, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "spectral_library", "unplaced_ptm_sites" ], "summary": "PXD018999 is a DDA label-free dataset (Mus musculus) with 48 runs, 48 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 974,746 PSMs, 78,290 peptidoforms and 8,239 protein groups, and the repository holds 46,440 PTM sites for it. 8 open warnings about it are recorded.", "page": "datasets/PXD018999.html", "json": "datasets/PXD018999.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018999.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD018999.json" }, { "dataset_id": "PXD019279", "title": "Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 51, "n_samples": 51, "n_psms_1pct": 1665837, "n_peptidoforms_1pct": 56523, "n_protein_groups_1pct": 5256, "n_ptm_sites": 46224, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD019279 is a DDA label-free dataset (Homo sapiens) with 51 runs, 51 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,665,837 PSMs, 56,523 peptidoforms and 5,256 protein groups, and the repository holds 46,224 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD019279.html", "json": "datasets/PXD019279.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD019279.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD019279.json" }, { "dataset_id": "PXD019849", "title": "Nerv. System Specific Yme1l KO (NYKO) Mice Retina Samples (30-31wks old)", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 10, "n_samples": 10, "n_psms_1pct": 668514, "n_peptidoforms_1pct": 68501, "n_protein_groups_1pct": 5975, "n_ptm_sites": 30700, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD019849 is a DDA label-free dataset (Mus musculus) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 668,514 PSMs, 68,501 peptidoforms and 5,975 protein groups, and the repository holds 30,700 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD019849.html", "json": "datasets/PXD019849.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD019849.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD019849.json" }, { "dataset_id": "PXD020462", "title": "Oxidative damage signatures in human bone collagen from Pompeii and Herculaneum.", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 4035, "n_peptidoforms_1pct": 457, "n_protein_groups_1pct": 46, "n_ptm_sites": 448, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "calibration_failed", "cysteine_poor", "high_contamination", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "peptide_rows_localization_ambiguous" ], "summary": "PXD020462 is a DDA label-free dataset (Homo sapiens) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 4,035 PSMs, 457 peptidoforms and 46 protein groups, and the repository holds 448 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD020462.html", "json": "datasets/PXD020462.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD020462.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD020462.json" }, { "dataset_id": "PXD021069", "title": "Matrix reverses immortalization-mediated stem cell fate determination", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 14, "n_samples": 14, "n_psms_1pct": 186914, "n_peptidoforms_1pct": 4690, "n_protein_groups_1pct": 1349, "n_ptm_sites": 3052, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD021069 is a DDA label-free dataset (Homo sapiens) with 14 runs, 14 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 186,914 PSMs, 4,690 peptidoforms and 1,349 protein groups, and the repository holds 3,052 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD021069.html", "json": "datasets/PXD021069.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD021069.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD021069.json" }, { "dataset_id": "PXD021762", "title": "Mitochondrial mistranslation is modulated by metabolic stress", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "other" ], "enrichment_mixed": false, "n_runs": 33, "n_samples": 33, "n_psms_1pct": 227290, "n_peptidoforms_1pct": 12628, "n_protein_groups_1pct": 1586, "n_ptm_sites": 8307, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD021762 is a DDA label-free dataset (Mus musculus) with 33 runs, 33 samples and an enrichment step outside the controlled list (recorded as `other`). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 227,290 PSMs, 12,628 peptidoforms and 1,586 protein groups, and the repository holds 8,307 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD021762.html", "json": "datasets/PXD021762.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD021762.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD021762.json" }, { "dataset_id": "PXD022128", "title": "A genome-wide screen for essentiality upon telomerase inhibition identifies a novel p53 regulator, C16ORF72/TAPR1", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "proximity_labelling" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 38855, "n_peptidoforms_1pct": 3389, "n_protein_groups_1pct": 1280, "n_ptm_sites": 1412, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD022128 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 38,855 PSMs, 3,389 peptidoforms and 1,280 protein groups, and the repository holds 1,412 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD022128.html", "json": "datasets/PXD022128.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022128.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022128.json" }, { "dataset_id": "PXD022180", "title": "Mytho, An Uncharacterized Gene that Controls Longevity and WIPI2-dependent Autophagy", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "immunoprecipitation" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 118902, "n_peptidoforms_1pct": 18717, "n_protein_groups_1pct": 1853, "n_ptm_sites": 9342, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "calibration_failed", "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD022180 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 118,902 PSMs, 18,717 peptidoforms and 1,853 protein groups, and the repository holds 9,342 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD022180.html", "json": "datasets/PXD022180.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022180.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022180.json" }, { "dataset_id": "PXD022196", "title": "Chaperone-mediated autophagy sustains hematopoietic stem cell function", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 32, "n_samples": 4, "n_psms_1pct": 250902, "n_peptidoforms_1pct": 26178, "n_protein_groups_1pct": 3800, "n_ptm_sites": 13517, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD022196 is a DDA label-free dataset (Mus musculus) with 32 runs, 4 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 250,902 PSMs, 26,178 peptidoforms and 3,800 protein groups, and the repository holds 13,517 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD022196.html", "json": "datasets/PXD022196.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022196.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022196.json" }, { "dataset_id": "PXD022227", "title": "Col4a5 mouse glomerular extracellular matrix", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 35, "n_samples": 35, "n_psms_1pct": 184016, "n_peptidoforms_1pct": 18035, "n_protein_groups_1pct": 2876, "n_ptm_sites": 9756, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "mbr_kept_exceeds_msms", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD022227 is a DDA label-free dataset (Mus musculus) with 35 runs, 35 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 184,016 PSMs, 18,035 peptidoforms and 2,876 protein groups, and the repository holds 9,756 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD022227.html", "json": "datasets/PXD022227.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022227.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022227.json" }, { "dataset_id": "PXD022363", "title": "Col4a1 mouse glomerular datasets", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 56170, "n_peptidoforms_1pct": 9054, "n_protein_groups_1pct": 1565, "n_ptm_sites": 4726, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD022363 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 56,170 PSMs, 9,054 peptidoforms and 1,565 protein groups, and the repository holds 4,726 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD022363.html", "json": "datasets/PXD022363.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022363.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022363.json" }, { "dataset_id": "PXD022393", "title": "Circadian Regulation of Protein Cargo in Exosomes", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 54, "n_samples": 54, "n_psms_1pct": 127036, "n_peptidoforms_1pct": 7456, "n_protein_groups_1pct": 1823, "n_ptm_sites": 7264, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD022393 is a DDA label-free dataset (Mus musculus) with 54 runs, 54 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 127,036 PSMs, 7,456 peptidoforms and 1,823 protein groups, and the repository holds 7,264 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD022393.html", "json": "datasets/PXD022393.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022393.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022393.json" }, { "dataset_id": "PXD022678", "title": "The landscape of molecular chaperones across human tissues reveals a layered architecture of core-variable chaperones", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 9, "n_samples": 9, "n_psms_1pct": 735560, "n_peptidoforms_1pct": 83172, "n_protein_groups_1pct": 5887, "n_ptm_sites": 47742, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD022678 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 735,560 PSMs, 83,172 peptidoforms and 5,887 protein groups, and the repository holds 47,742 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD022678.html", "json": "datasets/PXD022678.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022678.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022678.json" }, { "dataset_id": "PXD022737", "title": "proteomic changes in aging rats treated with the cognitive enhancer CE-123", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "other" ], "enrichment_mixed": false, "n_runs": 24, "n_samples": 24, "n_psms_1pct": 627316, "n_peptidoforms_1pct": 48822, "n_protein_groups_1pct": 4672, "n_ptm_sites": 33594, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD022737 is a DDA label-free dataset (Rattus norvegicus) with 24 runs, 24 samples and an enrichment step outside the controlled list (recorded as `other`). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 627,316 PSMs, 48,822 peptidoforms and 4,672 protein groups, and the repository holds 33,594 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD022737.html", "json": "datasets/PXD022737.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022737.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD022737.json" }, { "dataset_id": "PXD023381", "title": "Transcriptional and proteomic characterization of telomere-induced senescence in a human alveolar epithelial cell line", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 42734, "n_peptidoforms_1pct": 9844, "n_protein_groups_1pct": 1278, "n_ptm_sites": 5335, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD023381 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 42,734 PSMs, 9,844 peptidoforms and 1,278 protein groups, and the repository holds 5,335 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD023381.html", "json": "datasets/PXD023381.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD023381.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD023381.json" }, { "dataset_id": "PXD024216", "title": "Shotgun-based Proteomics of Extracellular Vesicles in Alzheimer’s Disease Reveals Biomarkers Involved in Immunological and Coagulation Pathways", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 57, "n_samples": 57, "n_psms_1pct": 181016, "n_peptidoforms_1pct": 5739, "n_protein_groups_1pct": 1260, "n_ptm_sites": 4438, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD024216 is a DDA label-free dataset (Homo sapiens) with 57 runs, 57 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 181,016 PSMs, 5,739 peptidoforms and 1,260 protein groups, and the repository holds 4,438 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD024216.html", "json": "datasets/PXD024216.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD024216.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD024216.json" }, { "dataset_id": "PXD024478", "title": "RNA polymerase I transcription disturbances lead to instable ribosomes in Cockayne syndrome", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 469358, "n_peptidoforms_1pct": 73419, "n_protein_groups_1pct": 7044, "n_ptm_sites": 32060, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "spectral_library", "unplaced_ptm_sites" ], "summary": "PXD024478 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 469,358 PSMs, 73,419 peptidoforms and 7,044 protein groups, and the repository holds 32,060 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD024478.html", "json": "datasets/PXD024478.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD024478.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD024478.json" }, { "dataset_id": "PXD024633", "title": "Mitochondrial mistranslation modulated by metabolic stress causes cardiovascular disease and reduced life-span", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 10, "n_samples": 10, "n_psms_1pct": 667123, "n_peptidoforms_1pct": 37083, "n_protein_groups_1pct": 3006, "n_ptm_sites": 14203, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD024633 is a DDA label-free dataset (Mus musculus) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 667,123 PSMs, 37,083 peptidoforms and 3,006 protein groups, and the repository holds 14,203 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD024633.html", "json": "datasets/PXD024633.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD024633.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD024633.json" }, { "dataset_id": "PXD024685", "title": "Proteomic analyses of non-preconditioned murine kidneys pre- and post-IRI in comparison to kidneys after preconditioning by hypoxia or caloric restriction", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 30, "n_samples": 30, "n_psms_1pct": 835173, "n_peptidoforms_1pct": 44479, "n_protein_groups_1pct": 4821, "n_ptm_sites": 21618, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD024685 is a DDA label-free dataset (Mus musculus) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 835,173 PSMs, 44,479 peptidoforms and 4,821 protein groups, and the repository holds 21,618 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD024685.html", "json": "datasets/PXD024685.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD024685.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD024685.json" }, { "dataset_id": "PXD024803", "title": "CHD6 IP from human induced pluripotent stem cells LC-MS-MS", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "immunoprecipitation" ], "enrichment_mixed": false, "n_runs": 28, "n_samples": 28, "n_psms_1pct": 381202, "n_peptidoforms_1pct": 37771, "n_protein_groups_1pct": 2202, "n_ptm_sites": 19715, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD024803 is a DDA label-free dataset (Homo sapiens) with 28 runs, 28 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 381,202 PSMs, 37,771 peptidoforms and 2,202 protein groups, and the repository holds 19,715 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD024803.html", "json": "datasets/PXD024803.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD024803.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD024803.json" }, { "dataset_id": "PXD025240", "title": "Hippocampal disruptions of synaptic and astrocyte metabolism during early amyloid pathology in the 5xFAD mouse model of Alzheimer’s disease", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 32, "n_samples": 32, "n_psms_1pct": 3136315, "n_peptidoforms_1pct": 80782, "n_protein_groups_1pct": 6942, "n_ptm_sites": 39456, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD025240 is a DDA label-free dataset (Mus musculus) with 32 runs, 32 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 3,136,315 PSMs, 80,782 peptidoforms and 6,942 protein groups, and the repository holds 39,456 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD025240.html", "json": "datasets/PXD025240.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD025240.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD025240.json" }, { "dataset_id": "PXD025280", "title": "Early- and late-passage primary human mesemchymal stem cells subjected to 2 hour heat shock", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 16, "n_samples": 16, "n_psms_1pct": 214292, "n_peptidoforms_1pct": 19885, "n_protein_groups_1pct": 3273, "n_ptm_sites": 8453, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD025280 is a DDA label-free dataset (Homo sapiens) with 16 runs, 16 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 214,292 PSMs, 19,885 peptidoforms and 3,273 protein groups, and the repository holds 8,453 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD025280.html", "json": "datasets/PXD025280.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD025280.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD025280.json" }, { "dataset_id": "PXD025321", "title": "Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 771808, "n_peptidoforms_1pct": 55484, "n_protein_groups_1pct": 4351, "n_ptm_sites": 27803, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD025321 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 771,808 PSMs, 55,484 peptidoforms and 4,351 protein groups, and the repository holds 27,803 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD025321.html", "json": "datasets/PXD025321.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD025321.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD025321.json" }, { "dataset_id": "PXD025503", "title": "Obesity causes irreversible mitochondria failure in visceral adipose tissue despite successful anti-obesogenic lifestyle", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 9, "n_samples": 9, "n_psms_1pct": 521289, "n_peptidoforms_1pct": 67071, "n_protein_groups_1pct": 4656, "n_ptm_sites": 34371, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD025503 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 521,289 PSMs, 67,071 peptidoforms and 4,656 protein groups, and the repository holds 34,371 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD025503.html", "json": "datasets/PXD025503.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD025503.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD025503.json" }, { "dataset_id": "PXD026219", "title": "Training-induced bioenergetic improvement in human skeletal muscle is associated with non-stoichiometric changes in the mitochondrial proteome without reorganisation of respiratory chain content", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 41, "n_samples": 41, "n_psms_1pct": 632869, "n_peptidoforms_1pct": 24889, "n_protein_groups_1pct": 2555, "n_ptm_sites": 21985, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD026219 is a DDA label-free dataset (Homo sapiens) with 41 runs, 41 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 632,869 PSMs, 24,889 peptidoforms and 2,555 protein groups, and the repository holds 21,985 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD026219.html", "json": "datasets/PXD026219.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD026219.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD026219.json" }, { "dataset_id": "PXD026335", "title": "Mouse Heart SS-31 Proteome and Phosphoproteome", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 940017, "n_peptidoforms_1pct": 63382, "n_protein_groups_1pct": 3805, "n_ptm_sites": 51105, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD026335 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 940,017 PSMs, 63,382 peptidoforms and 3,805 protein groups, and the repository holds 51,105 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD026335.html", "json": "datasets/PXD026335.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD026335.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD026335.json" }, { "dataset_id": "PXD026608", "title": "Integrated analysis of proteomics and phosphoproteomics on rat hearts with aging and hypertension", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 266155, "n_peptidoforms_1pct": 11560, "n_protein_groups_1pct": 2467, "n_ptm_sites": 14322, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD026608 is a DDA label-free dataset (Rattus norvegicus) with 12 runs, 12 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 266,155 PSMs, 11,560 peptidoforms and 2,467 protein groups, and the repository holds 14,322 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD026608.html", "json": "datasets/PXD026608.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD026608.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD026608.json" }, { "dataset_id": "PXD026934", "title": "Mitochondria regulate dietary lipid processing in enterocytes", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 904188, "n_peptidoforms_1pct": 83886, "n_protein_groups_1pct": 7573, "n_ptm_sites": 24351, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD026934 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 904,188 PSMs, 83,886 peptidoforms and 7,573 protein groups, and the repository holds 24,351 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD026934.html", "json": "datasets/PXD026934.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD026934.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD026934.json" }, { "dataset_id": "PXD027318", "title": "Identification of a Proteomic Signature of Senescence in Primary Human Mammary Epithelial Cells", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 378168, "n_peptidoforms_1pct": 49399, "n_protein_groups_1pct": 4478, "n_ptm_sites": 21704, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 3 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_design_file", "no_output_sdrf", "no_sdrf", "occupancy_decoy_groups", "unplaced_ptm_sites", "upstream_provenance_changed" ], "summary": "PXD027318 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 378,168 PSMs, 49,399 peptidoforms and 4,478 protein groups, and the repository holds 21,704 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD027318.html", "json": "datasets/PXD027318.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD027318.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD027318.json" }, { "dataset_id": "PXD027526", "title": "Mapping sites of carboxymethyllysine modification on proteins reveals consequences for proteostasis and cell proliferati", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 153, "n_samples": 153, "n_psms_1pct": 643119, "n_peptidoforms_1pct": 47450, "n_protein_groups_1pct": 6953, "n_ptm_sites": 23757, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "unplaced_ptm_sites" ], "summary": "PXD027526 is a DDA label-free dataset (Mus musculus) with 153 runs, 153 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 643,119 PSMs, 47,450 peptidoforms and 6,953 protein groups, and the repository holds 23,757 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD027526.html", "json": "datasets/PXD027526.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD027526.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD027526.json" }, { "dataset_id": "PXD027734", "title": "Proximity-biotinylation (BioID) to dissect cytoplasmic p53 signaling networks under nutrient stress", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "proximity_labelling" ], "enrichment_mixed": false, "n_runs": 19, "n_samples": 19, "n_psms_1pct": 487237, "n_peptidoforms_1pct": 63623, "n_protein_groups_1pct": 5374, "n_ptm_sites": 24722, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD027734 is a DDA label-free dataset (Homo sapiens) with 19 runs, 19 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 487,237 PSMs, 63,623 peptidoforms and 5,374 protein groups, and the repository holds 24,722 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD027734.html", "json": "datasets/PXD027734.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD027734.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD027734.json" }, { "dataset_id": "PXD027754", "title": "Metabolic reprogramming during hyperammonemia targets mitochondrial function and post-mitotic senescence", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 116756, "n_peptidoforms_1pct": 4281, "n_protein_groups_1pct": 487, "n_ptm_sites": 2532, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD027754 is a DDA label-free dataset (Rattus norvegicus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 116,756 PSMs, 4,281 peptidoforms and 487 protein groups, and the repository holds 2,532 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD027754.html", "json": "datasets/PXD027754.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD027754.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD027754.json" }, { "dataset_id": "PXD027971", "title": "Simple, single-shot phosphoproteomic analysis of heat-stable tau", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 247005, "n_peptidoforms_1pct": 16569, "n_protein_groups_1pct": 1184, "n_ptm_sites": 16641, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "cysteine_poor", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD027971 is a DDA label-free dataset (Rattus norvegicus) with 15 runs, 15 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 247,005 PSMs, 16,569 peptidoforms and 1,184 protein groups, and the repository holds 16,641 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD027971.html", "json": "datasets/PXD027971.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD027971.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD027971.json" }, { "dataset_id": "PXD028157", "title": "Proteomics quantification of striatal fraction from DAT-KO and WT rats", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 1351827, "n_peptidoforms_1pct": 56370, "n_protein_groups_1pct": 5126, "n_ptm_sites": 43069, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD028157 is a DDA label-free dataset (Rattus norvegicus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,351,827 PSMs, 56,370 peptidoforms and 5,126 protein groups, and the repository holds 43,069 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD028157.html", "json": "datasets/PXD028157.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD028157.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD028157.json" }, { "dataset_id": "PXD028590", "title": "Amphiregulin mediates non-cell-autonomous effect of senescence on reprogramming", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 24, "n_samples": 24, "n_psms_1pct": 487235, "n_peptidoforms_1pct": 38697, "n_protein_groups_1pct": 2560, "n_ptm_sites": 34170, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD028590 is a DDA label-free dataset (Mus musculus) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 487,235 PSMs, 38,697 peptidoforms and 2,560 protein groups, and the repository holds 34,170 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD028590.html", "json": "datasets/PXD028590.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD028590.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD028590.json" }, { "dataset_id": "PXD028852", "title": "Proteins enriched on damaged lysosomes in 293T", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "proximity_labelling" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 88611, "n_peptidoforms_1pct": 27920, "n_protein_groups_1pct": 2823, "n_ptm_sites": 8248, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD028852 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 88,611 PSMs, 27,920 peptidoforms and 2,823 protein groups, and the repository holds 8,248 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD028852.html", "json": "datasets/PXD028852.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD028852.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD028852.json" }, { "dataset_id": "PXD028865", "title": "Unbiased in vivo exploration of nuclear bodies-enhanced sumoylation reveals that PML orchestrates embryonic stem cell fa", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 32, "n_samples": 32, "n_psms_1pct": 1028186, "n_peptidoforms_1pct": 37114, "n_protein_groups_1pct": 3179, "n_ptm_sites": 30774, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD028865 is a DDA label-free dataset (Mus musculus) with 32 runs, 32 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,028,186 PSMs, 37,114 peptidoforms and 3,179 protein groups, and the repository holds 30,774 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD028865.html", "json": "datasets/PXD028865.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD028865.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD028865.json" }, { "dataset_id": "PXD028975", "title": "Engineering Extracellular Vesicles by Three-dimensional Dynamic Culture of Human Mesenchymal Stem Cells", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 30, "n_samples": 30, "n_psms_1pct": 563284, "n_peptidoforms_1pct": 15864, "n_protein_groups_1pct": 2055, "n_ptm_sites": 18331, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "spectral_library", "unplaced_ptm_sites" ], "summary": "PXD028975 is a DDA label-free dataset (Homo sapiens) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 563,284 PSMs, 15,864 peptidoforms and 2,055 protein groups, and the repository holds 18,331 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD028975.html", "json": "datasets/PXD028975.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD028975.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD028975.json" }, { "dataset_id": "PXD029116", "title": "Articular cartilage proteome differentiates by zones during osteoarthritis", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 30, "n_samples": 30, "n_psms_1pct": 66215, "n_peptidoforms_1pct": 4135, "n_protein_groups_1pct": 402, "n_ptm_sites": 3896, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 1 }, "finding_codes": [ "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD029116 is a DDA label-free dataset (Homo sapiens) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 66,215 PSMs, 4,135 peptidoforms and 402 protein groups, and the repository holds 3,896 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD029116.html", "json": "datasets/PXD029116.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD029116.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD029116.json" }, { "dataset_id": "PXD030773", "title": "The proto-oncogene TCL1A deregulates mitotic checkpoint transition and genomic stability in CLL", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 30, "n_samples": 30, "n_psms_1pct": 847058, "n_peptidoforms_1pct": 72404, "n_protein_groups_1pct": 5942, "n_ptm_sites": 35306, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD030773 is a DDA label-free dataset (Homo sapiens) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 847,058 PSMs, 72,404 peptidoforms and 5,942 protein groups, and the repository holds 35,306 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD030773.html", "json": "datasets/PXD030773.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD030773.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD030773.json" }, { "dataset_id": "PXD030776", "title": "The proto-oncogene TCL1A deregulates mitotic checkpoint transition and genomic stability in CLL", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "immunoprecipitation" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 139095, "n_peptidoforms_1pct": 14823, "n_protein_groups_1pct": 2111, "n_ptm_sites": 7684, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD030776 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 139,095 PSMs, 14,823 peptidoforms and 2,111 protein groups, and the repository holds 7,684 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD030776.html", "json": "datasets/PXD030776.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD030776.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD030776.json" }, { "dataset_id": "PXD030939", "title": "A compound-based therapy approach for epidermolysis bullosa simplex (EBS)", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": true, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 1169720, "n_peptidoforms_1pct": 125414, "n_protein_groups_1pct": 7958, "n_ptm_sites": 75247, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "mixed_enrichment", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD030939 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and runs that differ in enrichment (phospho on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,169,720 PSMs, 125,414 peptidoforms and 7,958 protein groups, and the repository holds 75,247 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD030939.html", "json": "datasets/PXD030939.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD030939.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD030939.json" }, { "dataset_id": "PXD031223", "title": "Chronic Aicar Treatment Identifies Sex-specific Phenotypes in the Aging Mouse Heart", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 8, "n_samples": 8, "n_psms_1pct": 125466, "n_peptidoforms_1pct": 6279, "n_protein_groups_1pct": 1324, "n_ptm_sites": 2326, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD031223 is a DDA label-free dataset (Mus musculus) with 8 runs, 8 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 125,466 PSMs, 6,279 peptidoforms and 1,324 protein groups, and the repository holds 2,326 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD031223.html", "json": "datasets/PXD031223.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD031223.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD031223.json" }, { "dataset_id": "PXD031604", "title": "Analysis of 20-HETE supplementation in calorically restricted C57Bl6 mice", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 1406442, "n_peptidoforms_1pct": 104634, "n_protein_groups_1pct": 6865, "n_ptm_sites": 55041, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "unplaced_ptm_sites" ], "summary": "PXD031604 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 1,406,442 PSMs, 104,634 peptidoforms and 6,865 protein groups, and the repository holds 55,041 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD031604.html", "json": "datasets/PXD031604.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD031604.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD031604.json" }, { "dataset_id": "PXD032040", "title": "Translational specialization in pluripotency by RBPMS poises future lineage-decisions", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "immunoprecipitation" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 118909, "n_peptidoforms_1pct": 21185, "n_protein_groups_1pct": 2538, "n_ptm_sites": 9604, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 3 }, "finding_codes": [ "collapsed_duplicate_rows", "contaminant_label_unresolved", "high_contamination", "no_design_file", "no_output_sdrf", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites", "upstream_provenance_changed" ], "summary": "PXD032040 is a DDA label-free dataset (Homo sapiens) with 15 runs, 15 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 118,909 PSMs, 21,185 peptidoforms and 2,538 protein groups, and the repository holds 9,604 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD032040.html", "json": "datasets/PXD032040.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032040.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032040.json" }, { "dataset_id": "PXD032044", "title": "Characterization of the skeletal muscle proteome in under-nourished old rats", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 44, "n_samples": 44, "n_psms_1pct": 871294, "n_peptidoforms_1pct": 38822, "n_protein_groups_1pct": 3003, "n_ptm_sites": 31761, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD032044 is a DDA label-free dataset (Rattus norvegicus) with 44 runs, 44 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 871,294 PSMs, 38,822 peptidoforms and 3,003 protein groups, and the repository holds 31,761 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD032044.html", "json": "datasets/PXD032044.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032044.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032044.json" }, { "dataset_id": "PXD032046", "title": "Translational specialization in pluripotency by RBPMS poises future lineage-decisions", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 144907, "n_peptidoforms_1pct": 26259, "n_protein_groups_1pct": 3751, "n_ptm_sites": 6003, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD032046 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 144,907 PSMs, 26,259 peptidoforms and 3,751 protein groups, and the repository holds 6,003 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD032046.html", "json": "datasets/PXD032046.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032046.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032046.json" }, { "dataset_id": "PXD032202", "title": "Global and comparative proteome signatures in the lens capsule, trabecular meshwork, and iris of patients with pseudoexfoliation glaucoma", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 21, "n_samples": 21, "n_psms_1pct": 183023, "n_peptidoforms_1pct": 21771, "n_protein_groups_1pct": 1925, "n_ptm_sites": 14088, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "count_mismatch", "no_design_file", "no_output_sdrf", "no_sdrf", "occupancy_decoy_groups", "unplaced_ptm_sites", "upstream_provenance_changed" ], "summary": "PXD032202 is a DDA label-free dataset (Homo sapiens) with 21 runs, 21 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 183,023 PSMs, 21,771 peptidoforms and 1,925 protein groups, and the repository holds 14,088 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD032202.html", "json": "datasets/PXD032202.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032202.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032202.json" }, { "dataset_id": "PXD032240", "title": "Unbiased in vivo exploration of nuclear bodies-enhanced sumoylation reveals that PML orchestrates embryonic stem cell fa", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 24, "n_samples": 24, "n_psms_1pct": 375188, "n_peptidoforms_1pct": 34716, "n_protein_groups_1pct": 3131, "n_ptm_sites": 25201, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD032240 is a DDA label-free dataset (Mus musculus) with 24 runs, 24 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 375,188 PSMs, 34,716 peptidoforms and 3,131 protein groups, and the repository holds 25,201 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD032240.html", "json": "datasets/PXD032240.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032240.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032240.json" }, { "dataset_id": "PXD032757", "title": "The role of extracellular vesicles in synovial fibroblast senescence", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 11, "n_samples": 11, "n_psms_1pct": 66715, "n_peptidoforms_1pct": 10546, "n_protein_groups_1pct": 1400, "n_ptm_sites": 6320, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD032757 is a DDA label-free dataset (Homo sapiens) with 11 runs, 11 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 66,715 PSMs, 10,546 peptidoforms and 1,400 protein groups, and the repository holds 6,320 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD032757.html", "json": "datasets/PXD032757.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032757.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD032757.json" }, { "dataset_id": "PXD033430", "title": "Dysregulated cellular redox status during hyperammonemia causes mitochondrial dysfunction by inhibiting sirtuin mediated", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "acetyl" ], "enrichment_mixed": false, "n_runs": 9, "n_samples": 9, "n_psms_1pct": 29476, "n_peptidoforms_1pct": 3084, "n_protein_groups_1pct": 1318, "n_ptm_sites": 2817, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD033430 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and enrichment: acetyl. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 29,476 PSMs, 3,084 peptidoforms and 1,318 protein groups, and the repository holds 2,817 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD033430.html", "json": "datasets/PXD033430.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD033430.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD033430.json" }, { "dataset_id": "PXD034432", "title": "Tracking prostate carcinogenesis over time through urine proteome profiling in an animal model: an exploratory approach", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 10, "n_samples": 10, "n_psms_1pct": 38154, "n_peptidoforms_1pct": 2836, "n_protein_groups_1pct": 608, "n_ptm_sites": 3363, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD034432 is a DDA label-free dataset (Rattus norvegicus) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 38,154 PSMs, 2,836 peptidoforms and 608 protein groups, and the repository holds 3,363 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD034432.html", "json": "datasets/PXD034432.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD034432.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD034432.json" }, { "dataset_id": "PXD034465", "title": "Surface proteome profiling of p53-restorable murine liver cancer cells", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 19, "n_samples": 19, "n_psms_1pct": 669101, "n_peptidoforms_1pct": 51806, "n_protein_groups_1pct": 4844, "n_ptm_sites": 22231, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD034465 is a DDA label-free dataset (Mus musculus) with 19 runs, 19 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 669,101 PSMs, 51,806 peptidoforms and 4,844 protein groups, and the repository holds 22,231 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD034465.html", "json": "datasets/PXD034465.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD034465.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD034465.json" }, { "dataset_id": "PXD034590", "title": "Profiling of purified autophagic vesicle content and degradome in the maturing and aging brain", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 81, "n_samples": 81, "n_psms_1pct": 2574920, "n_peptidoforms_1pct": 90744, "n_protein_groups_1pct": 6467, "n_ptm_sites": 43185, "sdrf_status": "partial", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_partial", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD034590 is a DDA label-free dataset (Mus musculus) with 81 runs, 81 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 2,574,920 PSMs, 90,744 peptidoforms and 6,467 protein groups, and the repository holds 43,185 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD034590.html", "json": "datasets/PXD034590.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD034590.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD034590.json" }, { "dataset_id": "PXD035107", "title": "Global phosphoproteomic profiling of skeletal muscle in ovarian-hormone deficient mice", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 8, "n_samples": 8, "n_psms_1pct": 69974, "n_peptidoforms_1pct": 12490, "n_protein_groups_1pct": 1442, "n_ptm_sites": 11612, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD035107 is a DDA label-free dataset (Mus musculus) with 8 runs, 8 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 69,974 PSMs, 12,490 peptidoforms and 1,442 protein groups, and the repository holds 11,612 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD035107.html", "json": "datasets/PXD035107.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035107.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035107.json" }, { "dataset_id": "PXD035149", "title": "ORP6 regulates astrocytic cholesterol metabolism and brain Aβ deposition", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 763140, "n_peptidoforms_1pct": 29089, "n_protein_groups_1pct": 3088, "n_ptm_sites": 25314, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD035149 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 763,140 PSMs, 29,089 peptidoforms and 3,088 protein groups, and the repository holds 25,314 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD035149.html", "json": "datasets/PXD035149.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035149.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035149.json" }, { "dataset_id": "PXD035171", "title": "Natural aging and ovariectomy induces parallel phosphoproteomic alterations \nin skeletal muscle of female mice", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 14, "n_samples": 14, "n_psms_1pct": 223143, "n_peptidoforms_1pct": 23287, "n_protein_groups_1pct": 1887, "n_ptm_sites": 16884, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "cysteine_poor", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD035171 is a DDA label-free dataset (Mus musculus) with 14 runs, 14 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 223,143 PSMs, 23,287 peptidoforms and 1,887 protein groups, and the repository holds 16,884 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD035171.html", "json": "datasets/PXD035171.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035171.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035171.json" }, { "dataset_id": "PXD035299", "title": "Nuclear protein expression profiling of IMR90 RAS cells compared to IMR90 Control cells", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "other" ], "enrichment_mixed": false, "n_runs": 10, "n_samples": 10, "n_psms_1pct": 1174457, "n_peptidoforms_1pct": 86978, "n_protein_groups_1pct": 5677, "n_ptm_sites": 37575, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "spectral_library", "unplaced_ptm_sites" ], "summary": "PXD035299 is a DDA label-free dataset (Homo sapiens) with 10 runs, 10 samples and an enrichment step outside the controlled list (recorded as `other`). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,174,457 PSMs, 86,978 peptidoforms and 5,677 protein groups, and the repository holds 37,575 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD035299.html", "json": "datasets/PXD035299.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035299.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035299.json" }, { "dataset_id": "PXD035412", "title": "Proteomics analysis of tissue aging nucleic acid binding proteins", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 30, "n_samples": 30, "n_psms_1pct": 1268270, "n_peptidoforms_1pct": 76470, "n_protein_groups_1pct": 6955, "n_ptm_sites": 64817, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD035412 is a DDA label-free dataset (Homo sapiens) with 30 runs, 30 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,268,270 PSMs, 76,470 peptidoforms and 6,955 protein groups, and the repository holds 64,817 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD035412.html", "json": "datasets/PXD035412.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035412.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035412.json" }, { "dataset_id": "PXD035446", "title": "Extracellular vesicle-derived miRNAs improve stem cell-based therapeutic approaches in muscle wasting conditions.", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 19796, "n_peptidoforms_1pct": 1487, "n_protein_groups_1pct": 235, "n_ptm_sites": 1169, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD035446 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 19,796 PSMs, 1,487 peptidoforms and 235 protein groups, and the repository holds 1,169 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD035446.html", "json": "datasets/PXD035446.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035446.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD035446.json" }, { "dataset_id": "PXD036557", "title": "Modelling Premature Cardiac Aging with Induced Pluripotent Stem Cells From a Hutchinson-Gilford Progeria Syndrome Patient", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 26582, "n_peptidoforms_1pct": 5541, "n_protein_groups_1pct": 1652, "n_ptm_sites": 2091, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "high_contamination", "low_id_rate", "no_design_file", "no_output_sdrf", "occupancy_decoy_groups", "sdrf_skeleton", "unplaced_ptm_sites", "upstream_provenance_changed" ], "summary": "PXD036557 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 26,582 PSMs, 5,541 peptidoforms and 1,652 protein groups, and the repository holds 2,091 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD036557.html", "json": "datasets/PXD036557.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD036557.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD036557.json" }, { "dataset_id": "PXD037230", "title": "Scleraxis-lineage cells are required for tendon homeostasis and their depletion induces an accelerated extracellular mat", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 303336, "n_peptidoforms_1pct": 15627, "n_protein_groups_1pct": 2283, "n_ptm_sites": 9419, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD037230 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 303,336 PSMs, 15,627 peptidoforms and 2,283 protein groups, and the repository holds 9,419 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD037230.html", "json": "datasets/PXD037230.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD037230.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD037230.json" }, { "dataset_id": "PXD038328", "title": "Organ protection by caloric restriction depends on activation of the de novo NAD+ synthesis pathway", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "acetyl" ], "enrichment_mixed": true, "n_runs": 40, "n_samples": 40, "n_psms_1pct": 1397244, "n_peptidoforms_1pct": 67381, "n_protein_groups_1pct": 4719, "n_ptm_sites": 48143, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "mixed_enrichment", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD038328 is a DDA label-free dataset (Mus musculus) with 40 runs, 40 samples and runs that differ in enrichment (acetyl on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,397,244 PSMs, 67,381 peptidoforms and 4,719 protein groups, and the repository holds 48,143 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD038328.html", "json": "datasets/PXD038328.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD038328.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD038328.json" }, { "dataset_id": "PXD038718", "title": "An NPAS4:NuA4 complex couples synaptic activity to DNA repair", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "immunoprecipitation" ], "enrichment_mixed": false, "n_runs": 14, "n_samples": 14, "n_psms_1pct": 40677, "n_peptidoforms_1pct": 8105, "n_protein_groups_1pct": 1754, "n_ptm_sites": 2256, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "cysteine_poor", "high_contamination", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD038718 is a DDA label-free dataset (Mus musculus) with 14 runs, 14 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 40,677 PSMs, 8,105 peptidoforms and 1,754 protein groups, and the repository holds 2,256 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD038718.html", "json": "datasets/PXD038718.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD038718.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD038718.json" }, { "dataset_id": "PXD039172", "title": "Proteome of the cortex of old Pink1-SNCA A53T double mutant Parkinson mice", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 98, "n_samples": 98, "n_psms_1pct": 1033275, "n_peptidoforms_1pct": 57636, "n_protein_groups_1pct": 6671, "n_ptm_sites": 41458, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "calibration_failed", "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD039172 is a DDA label-free dataset (Mus musculus) with 98 runs, 98 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,033,275 PSMs, 57,636 peptidoforms and 6,671 protein groups, and the repository holds 41,458 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD039172.html", "json": "datasets/PXD039172.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD039172.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD039172.json" }, { "dataset_id": "PXD041139", "title": "Proteomic analysis reveals insufficient folliculogenesis in Aging Female associates with infertility", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 14, "n_samples": 14, "n_psms_1pct": 432972, "n_peptidoforms_1pct": 8062, "n_protein_groups_1pct": 492, "n_ptm_sites": 10811, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD041139 is a DDA label-free dataset (Homo sapiens) with 14 runs, 14 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 432,972 PSMs, 8,062 peptidoforms and 492 protein groups, and the repository holds 10,811 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD041139.html", "json": "datasets/PXD041139.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD041139.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD041139.json" }, { "dataset_id": "PXD041376", "title": "Profiling of purified autophagic vesicle content and degradome in the maturing and aging brain - Part II", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 1665643, "n_peptidoforms_1pct": 57845, "n_protein_groups_1pct": 6181, "n_ptm_sites": 25872, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD041376 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,665,643 PSMs, 57,845 peptidoforms and 6,181 protein groups, and the repository holds 25,872 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD041376.html", "json": "datasets/PXD041376.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD041376.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD041376.json" }, { "dataset_id": "PXD041660", "title": "A Defective Extracellular Matrix/Kindlin-2/Actin/ERK Mechanosensing Pathway Affects Fibroblast-To-Myofibroblast Transiti", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 8, "n_samples": 8, "n_psms_1pct": 122316, "n_peptidoforms_1pct": 6419, "n_protein_groups_1pct": 1224, "n_ptm_sites": 2428, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD041660 is a DDA label-free dataset (Mus musculus) with 8 runs, 8 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 122,316 PSMs, 6,419 peptidoforms and 1,224 protein groups, and the repository holds 2,428 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD041660.html", "json": "datasets/PXD041660.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD041660.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD041660.json" }, { "dataset_id": "PXD041766", "title": "Remodeling of the focal adhesion complex by hydrogen-peroxide- induced senescence", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 8, "n_samples": 8, "n_psms_1pct": 199344, "n_peptidoforms_1pct": 36229, "n_protein_groups_1pct": 3372, "n_ptm_sites": 23381, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD041766 is a DDA label-free dataset (Mus musculus) with 8 runs, 8 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 199,344 PSMs, 36,229 peptidoforms and 3,372 protein groups, and the repository holds 23,381 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD041766.html", "json": "datasets/PXD041766.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD041766.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD041766.json" }, { "dataset_id": "PXD042301", "title": "Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process.", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "proximity_labelling" ], "enrichment_mixed": false, "n_runs": 31, "n_samples": 19, "n_psms_1pct": 363181, "n_peptidoforms_1pct": 31017, "n_protein_groups_1pct": 3712, "n_ptm_sites": 12533, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 4, "info": 3 }, "finding_codes": [ "collapsed_duplicate_rows", "contaminant_label_unresolved", "high_contamination", "no_design_file", "no_output_sdrf", "occupancy_decoy_groups", "unplaced_ptm_sites" ], "summary": "PXD042301 is a DDA label-free dataset (Mus musculus) with 31 runs, 19 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 363,181 PSMs, 31,017 peptidoforms and 3,712 protein groups, and the repository holds 12,533 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD042301.html", "json": "datasets/PXD042301.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD042301.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD042301.json" }, { "dataset_id": "PXD043001", "title": "Proteomic characterizationof the circle of Willis during aging", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 40, "n_samples": 40, "n_psms_1pct": 2821853, "n_peptidoforms_1pct": 75455, "n_protein_groups_1pct": 8548, "n_ptm_sites": 60348, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD043001 is a DDA label-free dataset (Mus musculus) with 40 runs, 40 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 2,821,853 PSMs, 75,455 peptidoforms and 8,548 protein groups, and the repository holds 60,348 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD043001.html", "json": "datasets/PXD043001.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD043001.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD043001.json" }, { "dataset_id": "PXD043644", "title": "Liver-derived plasminogen mediates muscle stem cell expansion during caloric restriction through the plasminogen recepto", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 88987, "n_peptidoforms_1pct": 1558, "n_protein_groups_1pct": 399, "n_ptm_sites": 2268, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored" ], "summary": "PXD043644 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 88,987 PSMs, 1,558 peptidoforms and 399 protein groups, and the repository holds 2,268 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD043644.html", "json": "datasets/PXD043644.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD043644.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD043644.json" }, { "dataset_id": "PXD043779", "title": "Evaluation of the secretome of senescent melanoma cells and the impact of silencing Mfn1 on the senescence-associated se", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 24, "n_samples": 24, "n_psms_1pct": 272721, "n_peptidoforms_1pct": 20697, "n_protein_groups_1pct": 2378, "n_ptm_sites": 11337, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD043779 is a DDA label-free dataset (Mus musculus) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 272,721 PSMs, 20,697 peptidoforms and 2,378 protein groups, and the repository holds 11,337 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD043779.html", "json": "datasets/PXD043779.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD043779.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD043779.json" }, { "dataset_id": "PXD043964", "title": "Luminal cerebrovascular proteomic changes during aging", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 32392, "n_peptidoforms_1pct": 7622, "n_protein_groups_1pct": 919, "n_ptm_sites": 3711, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD043964 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 32,392 PSMs, 7,622 peptidoforms and 919 protein groups, and the repository holds 3,711 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD043964.html", "json": "datasets/PXD043964.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD043964.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD043964.json" }, { "dataset_id": "PXD044227", "title": "Food perception liver phosphoproteome induced by caged food and POMC neuron activation", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 61, "n_samples": 61, "n_psms_1pct": 457219, "n_peptidoforms_1pct": 29973, "n_protein_groups_1pct": 4506, "n_ptm_sites": 23252, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "spectral_library", "unplaced_ptm_sites" ], "summary": "PXD044227 is a DDA label-free dataset (Mus musculus) with 61 runs, 61 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 457,219 PSMs, 29,973 peptidoforms and 4,506 protein groups, and the repository holds 23,252 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD044227.html", "json": "datasets/PXD044227.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD044227.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD044227.json" }, { "dataset_id": "PXD044453", "title": "Age-Dependent Effects of Voluntary Exercise on Urinary Voiding Function and Frailty-Related Metrics in Mice", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 40, "n_samples": 40, "n_psms_1pct": 164088, "n_peptidoforms_1pct": 2156, "n_protein_groups_1pct": 350, "n_ptm_sites": 4896, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD044453 is a DDA label-free dataset (Mus musculus) with 40 runs, 40 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 164,088 PSMs, 2,156 peptidoforms and 350 protein groups, and the repository holds 4,896 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD044453.html", "json": "datasets/PXD044453.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD044453.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD044453.json" }, { "dataset_id": "PXD044773", "title": "Cell-specific crosstalk proteomics reveals cathepsin B signaling as a driver of glioblastoma malignancy near the subventricular zone", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 21, "n_samples": 21, "n_psms_1pct": 423041, "n_peptidoforms_1pct": 33732, "n_protein_groups_1pct": 3645, "n_ptm_sites": 21783, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 8, "info": 2 }, "finding_codes": [ "contaminant_label_unresolved", "count_mismatch", "high_contamination", "no_design_file", "no_output_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites", "upstream_provenance_changed" ], "summary": "PXD044773 is a DDA label-free dataset (Homo sapiens) with 21 runs, 21 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 423,041 PSMs, 33,732 peptidoforms and 3,645 protein groups, and the repository holds 21,783 PTM sites for it. 8 open warnings about it are recorded.", "page": "datasets/PXD044773.html", "json": "datasets/PXD044773.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD044773.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD044773.json" }, { "dataset_id": "PXD044996", "title": "LC-MS/MS analysis of isolated murine brain endothelial cells (BECs) from 3-, 6-, 12-, and 18-months-old mice and Apoe-KO", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 25, "n_samples": 25, "n_psms_1pct": 285043, "n_peptidoforms_1pct": 37623, "n_protein_groups_1pct": 4166, "n_ptm_sites": 17804, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 9, "info": 2 }, "finding_codes": [ "calibration_failed", "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "low_core_use", "low_id_rate", "mbr_kept_exceeds_msms", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD044996 is a DDA label-free dataset (Mus musculus) with 25 runs, 25 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 285,043 PSMs, 37,623 peptidoforms and 4,166 protein groups, and the repository holds 17,804 PTM sites for it. 9 open warnings about it are recorded.", "page": "datasets/PXD044996.html", "json": "datasets/PXD044996.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD044996.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD044996.json" }, { "dataset_id": "PXD045821", "title": "Intracellular Iron Accumulation Facilitates Mycobacterial Infection in Old Mouse Macrophages", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 230387, "n_peptidoforms_1pct": 15385, "n_protein_groups_1pct": 3089, "n_ptm_sites": 8220, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD045821 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 230,387 PSMs, 15,385 peptidoforms and 3,089 protein groups, and the repository holds 8,220 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD045821.html", "json": "datasets/PXD045821.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD045821.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD045821.json" }, { "dataset_id": "PXD045861", "title": "Myelin-axon interface disruption uncovered by subcellular proteomics and imaging of Alzheimer’s human brain", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "proximity_labelling" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 1, "n_psms_1pct": 312904, "n_peptidoforms_1pct": 10572, "n_protein_groups_1pct": 2682, "n_ptm_sites": 10588, "sdrf_status": "partial", "findings_by_severity": { "error": 0, "warning": 9, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "sdrf_partial", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD045861 is a DDA label-free dataset (Homo sapiens) with 20 runs, 1 sample and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 312,904 PSMs, 10,572 peptidoforms and 2,682 protein groups, and the repository holds 10,588 PTM sites for it. 9 open warnings about it are recorded.", "page": "datasets/PXD045861.html", "json": "datasets/PXD045861.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD045861.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD045861.json" }, { "dataset_id": "PXD045887", "title": "An Intra-Individual Paired Mass Spectrometry dataset for decoding Solar-Induced Proteomic Changes in Facial Skin", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 40, "n_samples": 40, "n_psms_1pct": 416021, "n_peptidoforms_1pct": 6300, "n_protein_groups_1pct": 1164, "n_ptm_sites": 6098, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD045887 is a DDA label-free dataset (Homo sapiens) with 40 runs, 40 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 416,021 PSMs, 6,300 peptidoforms and 1,164 protein groups, and the repository holds 6,098 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD045887.html", "json": "datasets/PXD045887.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD045887.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD045887.json" }, { "dataset_id": "PXD047288", "title": "Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 36, "n_samples": 36, "n_psms_1pct": 8398, "n_peptidoforms_1pct": 884, "n_protein_groups_1pct": 367, "n_ptm_sites": 1602, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "cysteine_poor", "high_contamination", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD047288 is a DDA label-free dataset (Rattus norvegicus) with 36 runs, 36 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 8,398 PSMs, 884 peptidoforms and 367 protein groups, and the repository holds 1,602 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD047288.html", "json": "datasets/PXD047288.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD047288.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD047288.json" }, { "dataset_id": "PXD047289", "title": "Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 22, "n_samples": 11, "n_psms_1pct": 37693, "n_peptidoforms_1pct": 3402, "n_protein_groups_1pct": 1035, "n_ptm_sites": 2493, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD047289 is a DDA label-free dataset (Rattus norvegicus) with 22 runs, 11 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 37,693 PSMs, 3,402 peptidoforms and 1,035 protein groups, and the repository holds 2,493 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD047289.html", "json": "datasets/PXD047289.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD047289.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD047289.json" }, { "dataset_id": "PXD047292", "title": "Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 36, "n_samples": 18, "n_psms_1pct": 10059, "n_peptidoforms_1pct": 698, "n_protein_groups_1pct": 240, "n_ptm_sites": 1568, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "cysteine_poor", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD047292 is a DDA label-free dataset (Rattus norvegicus) with 36 runs, 18 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 10,059 PSMs, 698 peptidoforms and 240 protein groups, and the repository holds 1,568 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD047292.html", "json": "datasets/PXD047292.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD047292.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD047292.json" }, { "dataset_id": "PXD047293", "title": "Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 34, "n_samples": 18, "n_psms_1pct": 28664, "n_peptidoforms_1pct": 1714, "n_protein_groups_1pct": 486, "n_ptm_sites": 2039, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 8, "info": 3 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "excluded_from_search", "high_contamination", "low_core_use", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD047293 is a DDA label-free dataset (Rattus norvegicus) with 34 runs, 18 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 28,664 PSMs, 1,714 peptidoforms and 486 protein groups, and the repository holds 2,039 PTM sites for it. 8 open warnings about it are recorded.", "page": "datasets/PXD047293.html", "json": "datasets/PXD047293.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD047293.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD047293.json" }, { "dataset_id": "PXD048393", "title": "Acetyl-CoA Carboxylase Obstructs CD8+ T-Cell Lipid Utilization in the Tumor Microenvironment", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 1524774, "n_peptidoforms_1pct": 76022, "n_protein_groups_1pct": 6589, "n_ptm_sites": 56007, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD048393 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,524,774 PSMs, 76,022 peptidoforms and 6,589 protein groups, and the repository holds 56,007 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD048393.html", "json": "datasets/PXD048393.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD048393.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD048393.json" }, { "dataset_id": "PXD048720", "title": "Proteomic analysis of a rat streptozotocin model shows dysregulated biological pathways implicated in Alzheimer’s Disease", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 29, "n_samples": 29, "n_psms_1pct": 1325918, "n_peptidoforms_1pct": 41818, "n_protein_groups_1pct": 4202, "n_ptm_sites": 29907, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD048720 is a DDA label-free dataset (Rattus norvegicus) with 29 runs, 29 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,325,918 PSMs, 41,818 peptidoforms and 4,202 protein groups, and the repository holds 29,907 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD048720.html", "json": "datasets/PXD048720.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD048720.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD048720.json" }, { "dataset_id": "PXD048877", "title": "Egr1 is a master regulator of regenerative senescence and cardiac repair", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 30, "n_samples": 30, "n_psms_1pct": 1804710, "n_peptidoforms_1pct": 49168, "n_protein_groups_1pct": 4864, "n_ptm_sites": 37379, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD048877 is a DDA label-free dataset (Mus musculus) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,804,710 PSMs, 49,168 peptidoforms and 4,864 protein groups, and the repository holds 37,379 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD048877.html", "json": "datasets/PXD048877.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD048877.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD048877.json" }, { "dataset_id": "PXD049018", "title": "BJ cyto-nuclear translocation upon STING activation", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "proximity_labelling" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 104625, "n_peptidoforms_1pct": 17575, "n_protein_groups_1pct": 1626, "n_ptm_sites": 10007, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "spectral_library", "unplaced_ptm_sites" ], "summary": "PXD049018 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 104,625 PSMs, 17,575 peptidoforms and 1,626 protein groups, and the repository holds 10,007 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD049018.html", "json": "datasets/PXD049018.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD049018.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD049018.json" }, { "dataset_id": "PXD049957", "title": "Phosphoproteomics of consecuively active AKT in liver and Insulin stimulated primary Hepatocytes", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 34, "n_samples": 34, "n_psms_1pct": 1864731, "n_peptidoforms_1pct": 82701, "n_protein_groups_1pct": 7308, "n_ptm_sites": 55541, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD049957 is a DDA label-free dataset (Mus musculus) with 34 runs, 34 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,864,731 PSMs, 82,701 peptidoforms and 7,308 protein groups, and the repository holds 55,541 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD049957.html", "json": "datasets/PXD049957.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD049957.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD049957.json" }, { "dataset_id": "PXD050351", "title": "Targeting upstream Hippo-pathway kinases releases the scaffolder WWC1 to promote synaptic plasticity and long-term memory in mice", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "chemical_probe" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 213526, "n_peptidoforms_1pct": 15770, "n_protein_groups_1pct": 1481, "n_ptm_sites": 7765, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD050351 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and enrichment: chemical_probe. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 213,526 PSMs, 15,770 peptidoforms and 1,481 protein groups, and the repository holds 7,765 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD050351.html", "json": "datasets/PXD050351.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD050351.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD050351.json" }, { "dataset_id": "PXD051203", "title": "Protein degradation targets in the retrosplenial cortex of the female aged brain", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 39, "n_samples": 20, "n_psms_1pct": 34103, "n_peptidoforms_1pct": 3649, "n_protein_groups_1pct": 921, "n_ptm_sites": 2133, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "cysteine_poor", "excluded_from_search", "high_contamination", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD051203 is a DDA label-free dataset (Rattus norvegicus) with 39 runs, 20 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 34,103 PSMs, 3,649 peptidoforms and 921 protein groups, and the repository holds 2,133 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD051203.html", "json": "datasets/PXD051203.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD051203.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD051203.json" }, { "dataset_id": "PXD051644", "title": "Protein degradation targets in hippocampus of the aged brain following context exposure", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 23, "n_samples": 12, "n_psms_1pct": 23705, "n_peptidoforms_1pct": 1913, "n_protein_groups_1pct": 537, "n_ptm_sites": 1678, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 7, "info": 2 }, "finding_codes": [ "cysteine_poor", "excluded_from_search", "high_contamination", "low_core_use", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD051644 is a DDA label-free dataset (Rattus norvegicus) with 23 runs, 12 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 23,705 PSMs, 1,913 peptidoforms and 537 protein groups, and the repository holds 1,678 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD051644.html", "json": "datasets/PXD051644.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD051644.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD051644.json" }, { "dataset_id": "PXD051715", "title": "Age-related proteostatic imbalance exacerbates heart failure with preserved ejection fraction pathogenesis in old mice", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 21, "n_samples": 21, "n_psms_1pct": 1742303, "n_peptidoforms_1pct": 56195, "n_protein_groups_1pct": 3377, "n_ptm_sites": 45521, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD051715 is a DDA label-free dataset (Mus musculus) with 21 runs, 21 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,742,303 PSMs, 56,195 peptidoforms and 3,377 protein groups, and the repository holds 45,521 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD051715.html", "json": "datasets/PXD051715.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD051715.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD051715.json" }, { "dataset_id": "PXD052189", "title": "Microglial-derived C1q integrates into neuronal ribonucleoprotein complexes and impacts protein homeostasis in the aging", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "immunoprecipitation" ], "enrichment_mixed": false, "n_runs": 32, "n_samples": 32, "n_psms_1pct": 15718, "n_peptidoforms_1pct": 1752, "n_protein_groups_1pct": 577, "n_ptm_sites": 1456, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 8, "info": 2 }, "finding_codes": [ "calibration_failed", "contaminant_label_unresolved", "high_contamination", "low_id_rate", "no_design_file", "no_output_sdrf", "no_sdrf", "occupancy_decoy_groups", "unplaced_ptm_sites", "upstream_provenance_changed" ], "summary": "PXD052189 is a DDA label-free dataset (Mus musculus) with 32 runs, 32 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 15,718 PSMs, 1,752 peptidoforms and 577 protein groups, and the repository holds 1,456 PTM sites for it. 8 open warnings about it are recorded.", "page": "datasets/PXD052189.html", "json": "datasets/PXD052189.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD052189.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD052189.json" }, { "dataset_id": "PXD052631", "title": "G-CSF/NAMPT signaling drives neutrophil dysfunction and enhances bacterial infection susceptibility in cancer patients", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 22, "n_samples": 22, "n_psms_1pct": 41561, "n_peptidoforms_1pct": 3855, "n_protein_groups_1pct": 1003, "n_ptm_sites": 3303, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD052631 is a DDA label-free dataset (Mus musculus) with 22 runs, 22 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 41,561 PSMs, 3,855 peptidoforms and 1,003 protein groups, and the repository holds 3,303 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD052631.html", "json": "datasets/PXD052631.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD052631.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD052631.json" }, { "dataset_id": "PXD052797", "title": "Increased levels of extracellular matrix proteins in extracellular vesicles from brains of aged mice.", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 54, "n_samples": 54, "n_psms_1pct": 416306, "n_peptidoforms_1pct": 8103, "n_protein_groups_1pct": 1591, "n_ptm_sites": 9068, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD052797 is a DDA label-free dataset (Mus musculus) with 54 runs, 54 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 416,306 PSMs, 8,103 peptidoforms and 1,591 protein groups, and the repository holds 9,068 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD052797.html", "json": "datasets/PXD052797.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD052797.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD052797.json" }, { "dataset_id": "PXD053288", "title": "RyR2-mediated calcium leak increases glyoxalase I in the aging brain", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 660574, "n_peptidoforms_1pct": 57685, "n_protein_groups_1pct": 4947, "n_ptm_sites": 33379, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "cysteine_poor", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD053288 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 660,574 PSMs, 57,685 peptidoforms and 4,947 protein groups, and the repository holds 33,379 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD053288.html", "json": "datasets/PXD053288.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD053288.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD053288.json" }, { "dataset_id": "PXD054290", "title": "Mouse bone marrow-derived macrophages (BMDMs) loaded with atherogenic LDL", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 1403775, "n_peptidoforms_1pct": 30076, "n_protein_groups_1pct": 4144, "n_ptm_sites": 26926, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD054290 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,403,775 PSMs, 30,076 peptidoforms and 4,144 protein groups, and the repository holds 26,926 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD054290.html", "json": "datasets/PXD054290.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD054290.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD054290.json" }, { "dataset_id": "PXD055228", "title": "GPC3-mediated metabolic rewiring of diabetic mesenchymal stromal cells enhances their cardioprotective functions via pyr", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "immunoprecipitation" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 2687, "n_peptidoforms_1pct": 331, "n_protein_groups_1pct": 130, "n_ptm_sites": 267, "sdrf_status": "partial", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "high_contamination", "low_core_use", "low_id_rate", "mbr_kept_exceeds_msms", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_partial", "sdrf_uncoded" ], "summary": "PXD055228 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 2,687 PSMs, 331 peptidoforms and 130 protein groups, and the repository holds 267 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD055228.html", "json": "datasets/PXD055228.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD055228.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD055228.json" }, { "dataset_id": "PXD056276", "title": "SORLA upregulation suppresses global pathological effects in aged tauopathy mouse brain", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 26, "n_samples": 26, "n_psms_1pct": 961245, "n_peptidoforms_1pct": 22637, "n_protein_groups_1pct": 3959, "n_ptm_sites": 13265, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD056276 is a DDA label-free dataset (Mus musculus) with 26 runs, 26 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 961,245 PSMs, 22,637 peptidoforms and 3,959 protein groups, and the repository holds 13,265 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD056276.html", "json": "datasets/PXD056276.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD056276.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD056276.json" }, { "dataset_id": "PXD056433", "title": "M1 polyubiquitin targets in the hippocampus of young and aged male rats following contextual fear conditioning", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "other" ], "enrichment_mixed": false, "n_runs": 40, "n_samples": 20, "n_psms_1pct": 77681, "n_peptidoforms_1pct": 651, "n_protein_groups_1pct": 240, "n_ptm_sites": 1669, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "cysteine_poor", "low_core_use", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD056433 is a DDA label-free dataset (Rattus norvegicus) with 40 runs, 20 samples and an enrichment step outside the controlled list (recorded as `other`). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 77,681 PSMs, 651 peptidoforms and 240 protein groups, and the repository holds 1,669 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD056433.html", "json": "datasets/PXD056433.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD056433.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD056433.json" }, { "dataset_id": "PXD056458", "title": "M1 polyubiquitin targets in the hippocampus across the lifespan", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 38, "n_samples": 19, "n_psms_1pct": 118038, "n_peptidoforms_1pct": 978, "n_protein_groups_1pct": 357, "n_ptm_sites": 1962, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 4, "info": 1 }, "finding_codes": [ "cysteine_poor", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD056458 is a DDA label-free dataset (Rattus norvegicus) with 38 runs, 19 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 118,038 PSMs, 978 peptidoforms and 357 protein groups, and the repository holds 1,962 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD056458.html", "json": "datasets/PXD056458.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD056458.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD056458.json" }, { "dataset_id": "PXD057407", "title": "Proteomic and Phosphoproteomic Signatures of Aging Mouse Liver", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 10, "n_samples": 10, "n_psms_1pct": 921483, "n_peptidoforms_1pct": 29445, "n_protein_groups_1pct": 4258, "n_ptm_sites": 16734, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD057407 is a DDA label-free dataset (Mus musculus) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 921,483 PSMs, 29,445 peptidoforms and 4,258 protein groups, and the repository holds 16,734 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD057407.html", "json": "datasets/PXD057407.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057407.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057407.json" }, { "dataset_id": "PXD057409", "title": "Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease_C2C12 myotube p", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 9, "n_samples": 9, "n_psms_1pct": 484238, "n_peptidoforms_1pct": 44770, "n_protein_groups_1pct": 4053, "n_ptm_sites": 18842, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 1 }, "finding_codes": [ "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD057409 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 484,238 PSMs, 44,770 peptidoforms and 4,053 protein groups, and the repository holds 18,842 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD057409.html", "json": "datasets/PXD057409.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057409.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057409.json" }, { "dataset_id": "PXD057490", "title": "Synaptic phosphoproteome modifications and cortical circuit dysfunction are linked to the early-stage progression of alpha-synuclein pathology", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 8, "n_samples": 8, "n_psms_1pct": 93079, "n_peptidoforms_1pct": 6898, "n_protein_groups_1pct": 1944, "n_ptm_sites": 9155, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD057490 is a DDA label-free dataset (Rattus norvegicus) with 8 runs, 8 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 93,079 PSMs, 6,898 peptidoforms and 1,944 protein groups, and the repository holds 9,155 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD057490.html", "json": "datasets/PXD057490.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057490.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057490.json" }, { "dataset_id": "PXD057499", "title": "Synaptic phosphoproteome modifications and cortical circuit dysfunction are linked to the early-stage progression of alpha-synuclein pathology", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 8, "n_samples": 8, "n_psms_1pct": 249655, "n_peptidoforms_1pct": 19847, "n_protein_groups_1pct": 2865, "n_ptm_sites": 6985, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD057499 is a DDA label-free dataset (Rattus norvegicus) with 8 runs, 8 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 249,655 PSMs, 19,847 peptidoforms and 2,865 protein groups, and the repository holds 6,985 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD057499.html", "json": "datasets/PXD057499.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057499.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057499.json" }, { "dataset_id": "PXD057502", "title": "Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease-C2C12 myotube p", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 9, "n_samples": 9, "n_psms_1pct": 82421, "n_peptidoforms_1pct": 5962, "n_protein_groups_1pct": 2085, "n_ptm_sites": 7777, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD057502 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 82,421 PSMs, 5,962 peptidoforms and 2,085 protein groups, and the repository holds 7,777 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD057502.html", "json": "datasets/PXD057502.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057502.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057502.json" }, { "dataset_id": "PXD057544", "title": "Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease- C2C12 myotube ", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "acetyl" ], "enrichment_mixed": false, "n_runs": 9, "n_samples": 9, "n_psms_1pct": 26740, "n_peptidoforms_1pct": 2794, "n_protein_groups_1pct": 1223, "n_ptm_sites": 2489, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD057544 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and enrichment: acetyl. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 26,740 PSMs, 2,794 peptidoforms and 1,223 protein groups, and the repository holds 2,489 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD057544.html", "json": "datasets/PXD057544.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057544.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057544.json" }, { "dataset_id": "PXD057545", "title": "Chaperone-mediated autophagy sex-specifically regulates neuronal activity by remodeling the synaptic proteome", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 24, "n_samples": 24, "n_psms_1pct": 625331, "n_peptidoforms_1pct": 28590, "n_protein_groups_1pct": 3627, "n_ptm_sites": 13507, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD057545 is a DDA label-free dataset (Mus musculus) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 625,331 PSMs, 28,590 peptidoforms and 3,627 protein groups, and the repository holds 13,507 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD057545.html", "json": "datasets/PXD057545.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057545.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057545.json" }, { "dataset_id": "PXD057554", "title": "Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease-Mouse skeletal ", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 8, "n_samples": 8, "n_psms_1pct": 69522, "n_peptidoforms_1pct": 5699, "n_protein_groups_1pct": 720, "n_ptm_sites": 2646, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD057554 is a DDA label-free dataset (Mus musculus) with 8 runs, 8 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 69,522 PSMs, 5,699 peptidoforms and 720 protein groups, and the repository holds 2,646 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD057554.html", "json": "datasets/PXD057554.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057554.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD057554.json" }, { "dataset_id": "PXD058082", "title": "Major toxin composition of particulate matter from a coal-fired power plant and its proteomics-associated toxicological ", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 42223, "n_peptidoforms_1pct": 5087, "n_protein_groups_1pct": 1203, "n_ptm_sites": 1820, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "collapsed_duplicate_rows", "low_core_use", "low_id_rate", "no_sdrf", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD058082 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 42,223 PSMs, 5,087 peptidoforms and 1,203 protein groups, and the repository holds 1,820 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD058082.html", "json": "datasets/PXD058082.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058082.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058082.json" }, { "dataset_id": "PXD058156", "title": "Temozolomide Induces Glioblastoma Dedifferentiation into Highly Malignant Stem-like Cells Through Senescence-Associated Reprogramming via HIF1α/HIF2α Regulation", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 1049383, "n_peptidoforms_1pct": 83036, "n_protein_groups_1pct": 7570, "n_ptm_sites": 40180, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "spectral_library", "unplaced_ptm_sites" ], "summary": "PXD058156 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,049,383 PSMs, 83,036 peptidoforms and 7,570 protein groups, and the repository holds 40,180 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD058156.html", "json": "datasets/PXD058156.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058156.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058156.json" }, { "dataset_id": "PXD058248", "title": "K63 polyubiquitin targets in the hippocampus across the lifespan", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 38, "n_samples": 19, "n_psms_1pct": 43066, "n_peptidoforms_1pct": 629, "n_protein_groups_1pct": 239, "n_ptm_sites": 1955, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 4, "info": 1 }, "finding_codes": [ "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD058248 is a DDA label-free dataset (Rattus norvegicus) with 38 runs, 19 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 43,066 PSMs, 629 peptidoforms and 239 protein groups, and the repository holds 1,955 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD058248.html", "json": "datasets/PXD058248.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058248.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058248.json" }, { "dataset_id": "PXD058253", "title": "K63 polyubiquitin targets in the amygdala across the lifespan", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 38, "n_samples": 19, "n_psms_1pct": 12726, "n_peptidoforms_1pct": 234, "n_protein_groups_1pct": 139, "n_ptm_sites": 1541, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD058253 is a DDA label-free dataset (Rattus norvegicus) with 38 runs, 19 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 12,726 PSMs, 234 peptidoforms and 139 protein groups, and the repository holds 1,541 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD058253.html", "json": "datasets/PXD058253.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058253.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058253.json" }, { "dataset_id": "PXD058611", "title": "Enhanced non-enzymatic H2S generation extends lifespan and healthspan in male mice", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 194800, "n_peptidoforms_1pct": 15009, "n_protein_groups_1pct": 2126, "n_ptm_sites": 6146, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD058611 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 194,800 PSMs, 15,009 peptidoforms and 2,126 protein groups, and the repository holds 6,146 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD058611.html", "json": "datasets/PXD058611.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058611.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058611.json" }, { "dataset_id": "PXD058775", "title": "DNA Damage in Macrophages Drives Immune Autoreactivity via Nuclear Antigen Presentation", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "immunoprecipitation" ], "enrichment_mixed": false, "n_runs": 18, "n_samples": 18, "n_psms_1pct": 1859, "n_peptidoforms_1pct": 226, "n_protein_groups_1pct": 153, "n_ptm_sites": 128, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "calibration_failed", "contaminant_label_unresolved", "high_contamination", "low_id_rate", "no_design_file", "no_output_sdrf", "no_sdrf" ], "summary": "PXD058775 is a DDA label-free dataset (Mus musculus) with 18 runs, 18 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 1,859 PSMs, 226 peptidoforms and 153 protein groups, and the repository holds 128 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD058775.html", "json": "datasets/PXD058775.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058775.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058775.json" }, { "dataset_id": "PXD058855", "title": "KAT5-mediated acetylation of PC4 facilitates DNA repair by promoting chromatin reorganization", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 25, "n_samples": 25, "n_psms_1pct": 78573, "n_peptidoforms_1pct": 5632, "n_protein_groups_1pct": 1083, "n_ptm_sites": 4120, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD058855 is a DDA label-free dataset (Homo sapiens) with 25 runs, 25 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 78,573 PSMs, 5,632 peptidoforms and 1,083 protein groups, and the repository holds 4,120 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD058855.html", "json": "datasets/PXD058855.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058855.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058855.json" }, { "dataset_id": "PXD058971", "title": "Multi-omics Analysis Shed Light on the Extracellular Role of PCMT1", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 32, "n_samples": 32, "n_psms_1pct": 1549119, "n_peptidoforms_1pct": 120461, "n_protein_groups_1pct": 9704, "n_ptm_sites": 39912, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD058971 is a DDA label-free dataset (Mus musculus) with 32 runs, 32 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,549,119 PSMs, 120,461 peptidoforms and 9,704 protein groups, and the repository holds 39,912 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD058971.html", "json": "datasets/PXD058971.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058971.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD058971.json" }, { "dataset_id": "PXD059520", "title": "Retina-Targeted 17β-Estradiol by the DHED Prodrug Rescues Visual Function and Actuates Neuroprotective Protein Net-works after Optic Nerve Crush in a Rat Model of Surgical Menopause. Katalin Prokai-Tatrai, Khadiza Zaman, Ammar Kapic, Kelleigh Hogan , Gabriela Sanchez-Rodriguez, Anna E. Silverio Vien Nguyen , Laszlo Prokai and Andrew J. Feola", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 21, "n_samples": 21, "n_psms_1pct": 162200, "n_peptidoforms_1pct": 8846, "n_protein_groups_1pct": 1681, "n_ptm_sites": 5807, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD059520 is a DDA label-free dataset (Rattus norvegicus) with 21 runs, 21 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 162,200 PSMs, 8,846 peptidoforms and 1,681 protein groups, and the repository holds 5,807 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD059520.html", "json": "datasets/PXD059520.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD059520.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD059520.json" }, { "dataset_id": "PXD059818", "title": "Simultaneous profiling of native-state proteomes and transcriptomes of brain cell types using proximity labeling", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "proximity_labelling" ], "enrichment_mixed": false, "n_runs": 38, "n_samples": 38, "n_psms_1pct": 505085, "n_peptidoforms_1pct": 38626, "n_protein_groups_1pct": 4439, "n_ptm_sites": 20174, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD059818 is a DDA label-free dataset (Mus musculus) with 38 runs, 38 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 505,085 PSMs, 38,626 peptidoforms and 4,439 protein groups, and the repository holds 20,174 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD059818.html", "json": "datasets/PXD059818.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD059818.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD059818.json" }, { "dataset_id": "PXD060832", "title": "Mitochondrial regulator PGC-1a in neuronal metabolism and brain aging", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 15, "n_samples": 15, "n_psms_1pct": 151455, "n_peptidoforms_1pct": 6753, "n_protein_groups_1pct": 1746, "n_ptm_sites": 5137, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD060832 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 151,455 PSMs, 6,753 peptidoforms and 1,746 protein groups, and the repository holds 5,137 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD060832.html", "json": "datasets/PXD060832.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD060832.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD060832.json" }, { "dataset_id": "PXD060982", "title": "mTOR orchestrates sequential phases of ependymal cell differentiation by acting on their alternative cell cycle and cent", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 8, "n_samples": 8, "n_psms_1pct": 327734, "n_peptidoforms_1pct": 42460, "n_protein_groups_1pct": 6060, "n_ptm_sites": 49503, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD060982 is a DDA label-free dataset (Mus musculus) with 8 runs, 8 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 327,734 PSMs, 42,460 peptidoforms and 6,060 protein groups, and the repository holds 49,503 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD060982.html", "json": "datasets/PXD060982.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD060982.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD060982.json" }, { "dataset_id": "PXD061069", "title": "The SET1/COMPASS subunit RBBP5 orchestrates epigenetic control of global proteostasis and the 12h oscillator to safeguar", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "proximity_labelling" ], "enrichment_mixed": false, "n_runs": 120, "n_samples": 120, "n_psms_1pct": 586221, "n_peptidoforms_1pct": 35874, "n_protein_groups_1pct": 3220, "n_ptm_sites": 15631, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 8, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "low_id_rate", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD061069 is a DDA label-free dataset (Mus musculus) with 120 runs, 120 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 586,221 PSMs, 35,874 peptidoforms and 3,220 protein groups, and the repository holds 15,631 PTM sites for it. 8 open warnings about it are recorded.", "page": "datasets/PXD061069.html", "json": "datasets/PXD061069.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD061069.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD061069.json" }, { "dataset_id": "PXD061654", "title": "The mammalian longevity associated acetylome", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "acetyl" ], "enrichment_mixed": true, "n_runs": 30, "n_samples": 30, "n_psms_1pct": 2789721, "n_peptidoforms_1pct": 55792, "n_protein_groups_1pct": 3866, "n_ptm_sites": 36045, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "mixed_enrichment", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "unplaced_ptm_sites" ], "summary": "PXD061654 is a DDA label-free dataset (Mus musculus) with 30 runs, 30 samples and runs that differ in enrichment (acetyl on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 2,789,721 PSMs, 55,792 peptidoforms and 3,866 protein groups, and the repository holds 36,045 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD061654.html", "json": "datasets/PXD061654.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD061654.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD061654.json" }, { "dataset_id": "PXD064236", "title": "DLX2-FLAG IP-MS in embryonic bodies (EBs): Protein complexes identification", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "immunoprecipitation" ], "enrichment_mixed": false, "n_runs": 16, "n_samples": 16, "n_psms_1pct": 25389, "n_peptidoforms_1pct": 1752, "n_protein_groups_1pct": 509, "n_ptm_sites": 2336, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 7, "info": 1 }, "finding_codes": [ "count_mismatch", "cysteine_poor", "high_contamination", "low_id_rate", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD064236 is a DDA label-free dataset (Mus musculus) with 16 runs, 16 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 25,389 PSMs, 1,752 peptidoforms and 509 protein groups, and the repository holds 2,336 PTM sites for it. 7 open warnings about it are recorded.", "page": "datasets/PXD064236.html", "json": "datasets/PXD064236.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD064236.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD064236.json" }, { "dataset_id": "PXD067102", "title": "Young and aged T cells LC-MS/MS", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 1510240, "n_peptidoforms_1pct": 48026, "n_protein_groups_1pct": 5016, "n_ptm_sites": 45258, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD067102 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,510,240 PSMs, 48,026 peptidoforms and 5,016 protein groups, and the repository holds 45,258 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD067102.html", "json": "datasets/PXD067102.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD067102.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD067102.json" }, { "dataset_id": "PXD067622", "title": "DNA-Protein Crosslinks Promote cGAS-STING-driven Premature Aging and Embryonic Lethality", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "proximity_labelling" ], "enrichment_mixed": false, "n_runs": 24, "n_samples": 24, "n_psms_1pct": 623207, "n_peptidoforms_1pct": 44438, "n_protein_groups_1pct": 4167, "n_ptm_sites": 21493, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD067622 is a DDA label-free dataset (Homo sapiens) with 24 runs, 24 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 623,207 PSMs, 44,438 peptidoforms and 4,167 protein groups, and the repository holds 21,493 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD067622.html", "json": "datasets/PXD067622.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD067622.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD067622.json" }, { "dataset_id": "PXD068498", "title": "Reduced IGF-1 signaling fails to limit Alzheimer’s disease progression in a novel rat model of IGF-1R haploinsufficiency", "organisms": [ "NCBITaxon:10116" ], "organism_names": [ "Rattus norvegicus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 47, "n_samples": 47, "n_psms_1pct": 1143559, "n_peptidoforms_1pct": 24024, "n_protein_groups_1pct": 3969, "n_ptm_sites": 25440, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD068498 is a DDA label-free dataset (Rattus norvegicus) with 47 runs, 47 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,143,559 PSMs, 24,024 peptidoforms and 3,969 protein groups, and the repository holds 25,440 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD068498.html", "json": "datasets/PXD068498.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD068498.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD068498.json" }, { "dataset_id": "PXD069093", "title": "Kinome profiling of osteosarcoma patient-derived xenograft TT2 treated with palbociclib", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "affinity_purification" ], "enrichment_mixed": false, "n_runs": 16, "n_samples": 16, "n_psms_1pct": 490676, "n_peptidoforms_1pct": 22902, "n_protein_groups_1pct": 2078, "n_ptm_sites": 15824, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_skeleton", "unplaced_ptm_sites" ], "summary": "PXD069093 is a DDA label-free dataset (Homo sapiens) with 16 runs, 16 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 490,676 PSMs, 22,902 peptidoforms and 2,078 protein groups, and the repository holds 15,824 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD069093.html", "json": "datasets/PXD069093.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD069093.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD069093.json" }, { "dataset_id": "PXD071171", "title": "Mitochondrial IntegrityMitochondrial Integrity Modulates mTOR Signaling and Podocyte Function Modulates mTOR Signaling and Podocyte Function", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "phospho" ], "enrichment_mixed": false, "n_runs": 20, "n_samples": 20, "n_psms_1pct": 662717, "n_peptidoforms_1pct": 79897, "n_protein_groups_1pct": 7785, "n_ptm_sites": 56740, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 4, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD071171 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 662,717 PSMs, 79,897 peptidoforms and 7,785 protein groups, and the repository holds 56,740 PTM sites for it. 4 open warnings about it are recorded.", "page": "datasets/PXD071171.html", "json": "datasets/PXD071171.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD071171.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD071171.json" }, { "dataset_id": "PXD073846", "title": "mtDNA alterations determine myoblast differentiation and disrupt skeletal muscle architecture", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "proximity_labelling" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 171140, "n_peptidoforms_1pct": 23990, "n_protein_groups_1pct": 2307, "n_ptm_sites": 9019, "sdrf_status": "trusted", "findings_by_severity": { "error": 0, "warning": 6, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "low_core_use", "occupancy_decoy_groups", "occupancy_not_stored", "sdrf_uncoded", "unplaced_ptm_sites" ], "summary": "PXD073846 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 171,140 PSMs, 23,990 peptidoforms and 2,307 protein groups, and the repository holds 9,019 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD073846.html", "json": "datasets/PXD073846.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD073846.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD073846.json" }, { "dataset_id": "PXD073999", "title": "Mechanisms of the antiproliferative effects of SIRT6 inhibition in melanoma: A multi-omics analysis", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 12, "n_samples": 12, "n_psms_1pct": 514178, "n_peptidoforms_1pct": 26734, "n_protein_groups_1pct": 3232, "n_ptm_sites": 15329, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 6, "info": 1 }, "finding_codes": [ "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "peptide_rows_localization_ambiguous", "unplaced_ptm_sites" ], "summary": "PXD073999 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 514,178 PSMs, 26,734 peptidoforms and 3,232 protein groups, and the repository holds 15,329 PTM sites for it. 6 open warnings about it are recorded.", "page": "datasets/PXD073999.html", "json": "datasets/PXD073999.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD073999.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD073999.json" }, { "dataset_id": "PXD075372", "title": "Senescence inhibition by rapamycin mitigates radiation-induced atherosclerosis characteristics in human coronary endothelial cells", "organisms": [ "NCBITaxon:9606" ], "organism_names": [ "Homo sapiens" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 24, "n_samples": 24, "n_psms_1pct": 1107679, "n_peptidoforms_1pct": 77281, "n_protein_groups_1pct": 6036, "n_ptm_sites": 73987, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "low_core_use", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD075372 is a DDA label-free dataset (Homo sapiens) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,107,679 PSMs, 77,281 peptidoforms and 6,036 protein groups, and the repository holds 73,987 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD075372.html", "json": "datasets/PXD075372.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD075372.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD075372.json" }, { "dataset_id": "PXD077298", "title": "Sinapic acid promotes disaggregation and extracellular secretion of polyglutamine repeats containing aggregates and resc", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "immunoprecipitation", "other" ], "enrichment_mixed": true, "n_runs": 22, "n_samples": 22, "n_psms_1pct": 239229, "n_peptidoforms_1pct": 37276, "n_protein_groups_1pct": 4716, "n_ptm_sites": 17144, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 8, "info": 1 }, "finding_codes": [ "count_mismatch", "high_contamination", "low_core_use", "mixed_enrichment", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD077298 is a DDA label-free dataset (Mus musculus) with 22 runs, 22 samples and runs that differ in enrichment (immunoprecipitation and other on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 239,229 PSMs, 37,276 peptidoforms and 4,716 protein groups, and the repository holds 17,144 PTM sites for it. 8 open warnings about it are recorded.", "page": "datasets/PXD077298.html", "json": "datasets/PXD077298.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD077298.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD077298.json" }, { "dataset_id": "PXD082596", "title": "Proteomic comparison of tail tendons from Col1a2 mutant mice", "organisms": [ "NCBITaxon:10090" ], "organism_names": [ "Mus musculus" ], "acquisition": "DDA", "quant_method": "label_free", "labelling": "none", "enrichment": [ "none" ], "enrichment_mixed": false, "n_runs": 24, "n_samples": 24, "n_psms_1pct": 472890, "n_peptidoforms_1pct": 23266, "n_protein_groups_1pct": 3375, "n_ptm_sites": 11841, "sdrf_status": "absent", "findings_by_severity": { "error": 0, "warning": 5, "info": 2 }, "finding_codes": [ "collapsed_duplicate_rows", "count_mismatch", "high_contamination", "no_sdrf", "occupancy_decoy_groups", "occupancy_not_stored", "unplaced_ptm_sites" ], "summary": "PXD082596 is a DDA label-free dataset (Mus musculus) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 472,890 PSMs, 23,266 peptidoforms and 3,375 protein groups, and the repository holds 11,841 PTM sites for it. 5 open warnings about it are recorded.", "page": "datasets/PXD082596.html", "json": "datasets/PXD082596.json", "page_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD082596.html", "json_url": "https://trishorts.github.io/aging-pipeline/datasets/PXD082596.json" } ] }