Do organelles age at different rates?
This is the data repository of an NCEMS working group on aging. The group asks whether organelles age at different rates, and whether proteoform- and PTM-level measurements can see aging signal that bulk protein abundance misses.
To answer that, it reanalyses public aging proteomics data from PRIDE with one pipeline, so that datasets from different labs, instruments and years can be compared. Every dataset is searched from its raw spectra, never from the authors' processed tables, and every number keeps a record of the exact files, tools and settings that made it.
How it works
- aging-pipeline finds aging datasets in PRIDE, downloads and quality-checks the raw spectra, and searches and quantifies them with MetaMorpheus, including GPTMD to discover post-translational modifications, and FlashLFQ.
- dataRepo stores the results in one schema and serves them to people and to AI agents. This site is generated from its catalog.
Where it stands
- 189 datasets, 121 of them whole proteomes (no enrichment step): mouse 101 (69 whole); human 62 (40 whole); rat 26 (12 whole).
- Enrichments: affinity_purification 20; phospho 12; proximity_labelling 10; immunoprecipitation 9; mixed runs 7; other 5; chemical_probe 3; acetyl 2.
- Beyond identifications and quantities: per-run PTM site occupancy (8,092,518 rows, 189 datasets) and protein-to-gene mappings (3,115,514 rows). These, and every individual protein, are in the catalog and reachable through the MCP server, not on these pages. The catalog file itself is not published yet.
- Sample ages: 192 runs in PXD047288, PXD047289, PXD047292, PXD047293, PXD051203, PXD051644, PXD056433, PXD056458, PXD058248, PXD058253, curated from the depositors' own records and paper.
- Organelle assignments: GO cellular-component terms for the proteins of 189 datasets (21,227,308 rows), grouped into 12 organelle categories (aging-organelle-map v1, GO releases/2026-07-26). Each row keeps its own GO evidence code.
- Not held yet: age effects, and an experimental design for any dataset. Every dataset was quantified with each raw file as its own condition.
- These counts are from catalog
2acdd821cb79c4bc.
So the repository cannot answer the group's question on its own yet: ages, designs and organelle assignments are the next stages of the pipeline. Each dataset page lists the known problems with that dataset. Please read them before using its numbers.
Use it with your own AI agent
Any assistant that can read a web page (Claude, ChatGPT, Gemini, or your own agent with a fetch tool) can work from this site. There is nothing to install.
- Start here. Begin your conversation with: "Read https://trishorts.github.io/aging-pipeline/llms.txt and follow its rules. Then answer: ...".
llms.txtlists every dataset with a one-sentence summary, and the rules that keep answers honest. - For one dataset's details, use its page:
https://trishorts.github.io/aging-pipeline/datasets/<accession>.html(for exampledatasets/PXD036557.html). Each page gives the dataset's counts, quality metrics, most frequent modifications and every known problem. - Prefer the pages to
datasets.json. It holds the same facts for every dataset in one file, but it is large enough that many fetch tools cut it off without saying so, and an agent can then miss datasets without knowing. - Ask it to cite. Every number here comes from one catalog build. Have your agent quote the catalog id shown above with any number it reuses.
Questions that work from these pages today:
- "Which datasets in this repository are whole-proteome mouse samples?"
- "Which dataset has the most PSMs at 1% FDR, and how many?"
- "Why does PXD051644 have fewer runs than PRIDE lists?"
- "What are the open warnings for PXD036557, and what do they mean for using its numbers?"
- "Which datasets have sample ages?"
Protein-level questions need more than the website (next section). Until then, "not available from the site" is the correct answer to a protein-level question, and a good agent will say so.
How you will be able to query the full catalog (not available yet)
None of this works yet. The catalog is a single database file (DuckDB) too large for this website, and it is not yet on a public server. When it is, the link and install instructions will appear here, and the steps will be:
- Download the catalog file. It is one file, named after the catalog id shown above.
- Install the repository's query tool (instructions will come with the download; note that an unrelated package with the same name exists on PyPI).
- Connect your agent. For Claude Code:
datarepo mcp --catalog <file> --install, then restart Claude Code. For any other assistant that supports MCP servers, adddatarepo mcp --catalog <file>as a local (stdio) server.datarepo mcp --catalog <file> --checkconfirms the file opens. - Or query it directly with DuckDB and SQL. The
*_1pctviews (psms_1pct,peptidoforms_1pct,protein_groups_1pct) already apply the 1% FDR rule.
Your agent then gets three tools: describe (what the catalog holds, and what every table and column means), search (look up a dataset, protein, gene, peptide or modification) and sql (read-only queries). The biology it is built for:
- Does aging change how proteins are tagged, not just how much? "Across the four rat hippocampus and cortex lifespan datasets (3, 12 and 24 months), which proteins gain degradation tags (K48 polyubiquitin) with age, and are they the same ones that lose signalling tags (M1 and K63)?"
- Aging that abundance clocks cannot see. "In the rat lifespan datasets, which modification sites change in how often they are occupied between young and old animals while the protein's own amount stays flat?"
- Molecular timers. "Within the lens and cartilage datasets, do long-lived proteins such as crystallins and collagens carry more asparagine deamidation, a spontaneous chemical clock, than short-lived proteins from the same tissue?"
- The senescent cell. "In senescent versus young human mammary epithelial cells (PXD027318; the run names mark the groups), do lysosomal proteins rise and does the nuclear lamina protein lamin B1 fall?"
- Organelles in the aging human heart (the dataset is being added): "In the human left ventricle, do mitochondrial proteins decline with age faster than the rest of the proteome, in failing and non-failing hearts alike?"
Every answer is exploratory. The datasets are small, and the sample ages are curated by hand from each deposit's own paper and record. Most of the rat datasets are ubiquitin pulldowns rather than whole tissue, so a change there means a change in what was tagged, not in how much of the protein exists.
Before you use these numbers
- A dataset's organism is the species of the protein database it was searched against. It is not an independent check of the sample, and no cell line or tissue is recorded yet. Where a title disagrees (PXD050351 says "in mice"; its samples are a human cell line), the searched species is the one to trust.
- A deposited SDRF labels the samples; it is not an experimental design. Where one exists it names organism, tissue and replicate, and no dataset has conditions assigned to runs yet.
- Protein-group counts at 1% FDR include contaminant groups. The MCP server's views say so and let you separate them.
- In mouse and rat datasets, some groups labelled contaminant are native proteins. The search's contaminant panel carries some ordinary human proteins (for example tau, creatine kinase M and peroxiredoxin-1), and rodent peptides shared with them are credited to the panel. Contamination figures for those datasets are therefore somewhat overstated.
- One chemistry can appear under two modification names (phosphoserine is listed both under its UniProt name and its search-engine name). Count by chemistry, not by name.
Many datasets are enrichments, not whole proteomes. Immunoprecipitations, proximity-labelling and affinity pulldowns, and chemical-probe captures are kept, because an organelle pulldown is an organelle proteome, and each is labelled with its enrichment. Their intensities describe the captured material. Do not read them as whole-cell abundance, or pool them with whole proteomes.
Built at the Smith lab, University of Wisconsin–Madison. Questions and problems: please open an issue on aging-pipeline.
Datasets
189
public PRIDE datasets, each reanalysed from its raw files
Raw files searched
4,707
LC-MS/MS runs
Spectra searched
230M
MS2 scans in the raw files, summed (aging:DEF-MS2)
PSMs at 1% FDR
99.2M
target peptide-spectrum matches, as the search engine counts them
Unique peptides at 1% FDR
699K
peptide sequences found in a single gene's proteins in the searched databases, in every dataset that found them, decoys and contaminants excluded; out of 731,333 sequences in all
Proteins identified
46.6K
accessions with 1%-FDR evidence, decoys and contaminants excluded; 9,885 of them in 24 or more datasets
Proteins, whole-proteome datasets
44K
the same count over the 121 datasets with no enrichment step; an enriched dataset (pull-down, probe, IP) says nothing about the proteome
PTM sites
3.6M
modified residues on proteins, 183 kinds of modification; on target proteins, 269,991 phosphorylation (UNIMOD:21) and 119,968 acetylation (UNIMOD:1) sites
Figures of merit from catalog 2acdd821cb79c4bc. Hover a number for its exact value.
This repository
Search and quantification results for 189 public proteomics datasets, reanalysed with one pipeline and stored with the same schema, so they can be compared. The question they serve is how organelle proteomes change with age.
For AI agents: start at llms.txt. The same facts
as this page are in datasets.json.
The corpus at a glance
| Organism searched | none | acetyl | acetyl (on some runs only; runs differ) | affinity_purification | chemical_probe | immunoprecipitation | immunoprecipitation, other (on some runs only; runs differ) | other | other (on some runs only; runs differ) | phospho | phospho (on some runs only; runs differ) | proximity_labelling | ubiquitin_GG (on some runs only; runs differ) | All |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Homo sapiens | 40 | 5 | 3 | 4 | 2 | 1 | 1 | 6 | 62 | |||||
| Mus musculus | 69 | 2 | 2 | 6 | 5 | 1 | 1 | 1 | 8 | 1 | 4 | 1 | 101 | |
| Rattus norvegicus | 12 | 9 | 2 | 3 | 26 |
Datasets by the organism of the searched database and the declared enrichment. "none" is a whole-proteome dataset; any other value is a capture, and a protein's absence from one says nothing about the proteome.
Datasets
Counts are at 1% FDR, as the search engine reports them. "Findings" are what is recorded against a dataset, by type; most are about what the deposit lacks (no SDRF, no design). Read them before using it. Organism is that of the protein database searched.
| Dataset | Title | Organism | Enrichment | Runs | PSMs | Protein groups | PTM sites | Findings |
|---|---|---|---|---|---|---|---|---|
| PXD001054 | Redox Proteome of Skeletal Muscle | Mus musculus | none | 9 | 55,829 | 912 | 4,450 | 0 E / 4 W / 1 I count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD002467 | Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats | Rattus norvegicus | none | 96 | 1,453,769 | 6,747 | 29,726 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD004916 | Spermidine treated mouse Heart LC-MS/MS | Mus musculus | none | 54 | 227,597 | 2,001 | 5,536 | 0 E / 8 W / 1 I contaminant_label_unresolved, cysteine_poor, high_contamination, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites, upstream_provenance_changed |
| PXD005014 | Proteome of Young and Old Murine Diaphragm and Associaated Changes in Contractile Properties | Mus musculus | none | 12 | 115,772 | 1,368 | 4,483 | 0 E / 4 W / 1 I count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD005123 | Somatic increase of CCT8 mimics proteostasis of human pluripotent stem cells and extends C. elegans lifespan | Homo sapiens | none | 20 | 1,101,243 | 7,889 | 25,195 | 0 E / 6 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, unplaced_ptm_sites |
| PXD006023 | AGK human LC-MSMS project part I (proteome) | Homo sapiens | other | 18 | 767,748 | 5,347 | 13,244 | 0 E / 6 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, unplaced_ptm_sites |
| PXD006216 | Chemotherapy-induced cellular senescence is characterized by aberrant lipid regulation and lipid peroxidation | Mus musculus | none | 30 | 272,722 | 3,979 | 18,744 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD006578 | Aging-related proteome alterations in B cells may predispose for chronic lymphocytic leukemia - cytoplasmic proteins of CLL cells | Homo sapiens | none | 18 | 671,443 | 6,127 | 33,985 | 0 E / 6 W / 1 I count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, unplaced_ptm_sites |
| PXD006589 | Aging-related proteome alterations in B cells may predispose for chronic lymphocytic leukemia - nuclear proteins of CLL cells | Homo sapiens | none | 18 | 546,673 | 5,244 | 27,252 | 0 E / 6 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, unplaced_ptm_sites |
| PXD006815 | Changes in glycogen metabolism machinery are associated with brain aging. Proteomic and immunofluorescent evidence for a | Mus musculus | none | 36 | 1,142,250 | 7,685 | 40,002 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, cysteine_poor, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD006898 | Quantitative proteomics of a human fetal ovary development timecourse | Homo sapiens | none | 15 | 618,984 | 6,520 | 31,076 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD007035 | Loss-of-function of ubiquitin ligase adaptor LZTR1 triggers human disease by dysregulating RAS ubiquitination | Mus musculus | ubiquitin_GG (on some runs only; runs differ) | 12 | 126,015 | 3,836 | 9,575 | 0 E / 6 W / 1 I high_contamination, low_core_use, mixed_enrichment, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD007049 | Loss-of-function of ubiquitin ligase adaptor LZTR1 triggers human disease by dysregulating RAS ubiquitination | Homo sapiens | affinity_purification | 12 | 22,417 | 781 | 1,827 | 0 E / 7 W / 1 I count_mismatch, cysteine_poor, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD007188 | Mevalonate pathway activity is a key determinant of radiation sensitivity in head and neck cancer | Homo sapiens | none | 18 | 329,746 | 5,704 | 27,637 | 0 E / 5 W / 1 I count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD007906 | A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cell line | Homo sapiens | none | 24 | 882,422 | 3,487 | 26,288 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD007999 | NRF2-dependent ECM - Nrf2-Mediated Fibroblast Reprogramming Drives Cellular Senescence by Targeting the Matrisome | Mus musculus | none | 30 | 404,489 | 4,031 | 20,858 | 0 E / 7 W / 2 I contaminant_label_unresolved, count_mismatch, high_contamination, no_design_file, no_output_sdrf, no_sdrf, occupancy_decoy_groups, unplaced_ptm_sites, upstream_provenance_changed |
| PXD008050 | UVA and to UV-oxidized lipids proteomic regulation of the human keratinocytes | Homo sapiens | none | 18 | 937,570 | 5,614 | 40,949 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD008344 | Human brain LC-MS/MS - Brain Citrullination Patterns and T Cell Reactivity of Cerebrospinal Fluid-Derived CD4+ T Cells in Multiple Sclerosis | Homo sapiens | none | 44 | 766,417 | 8,640 | 61,855 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD008934 | Characterization of proteomic changes in human heart failure | Homo sapiens | none | 34 | 1,832,742 | 4,532 | 66,232 | 0 E / 3 W / 2 I collapsed_duplicate_rows, count_mismatch, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD008990 | Glycomic and Proteomic changes in aging brain nigrostriatal pathway | Rattus norvegicus | none | 70 | 534,367 | 2,195 | 3,558 | 0 E / 6 W / 1 I count_mismatch, cysteine_poor, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD009212 | Proteome profiling in aging rat brain by LC-MS/MS | Rattus norvegicus | none | 57 | 195,142 | 1,711 | 5,753 | 0 E / 7 W / 1 I high_contamination, low_core_use, low_id_rate, mbr_kept_exceeds_msms, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD009430 | Modulation of the ATM / autophagy pathway tips the balance between senescence and apoptosis in response to a quadruplex ligand | Homo sapiens | none | 12 | 301,057 | 2,782 | 16,167 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, spectral_library, unplaced_ptm_sites |
| PXD010091 | miR-181a Restores Mitochondrial Dynamics in Skeletal Muscle Ageing | Mus musculus | none | 20 | 217,078 | 1,402 | 6,526 | 0 E / 5 W / 1 I count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD010115 | Quantification of the Soluble Receptor of Advanced Glycation End-Products (sRAGE) by LC-MS Without the Use of Affinity Enrichment | Homo sapiens | none | 12 | 119,030 | 445 | 7,952 | 0 E / 7 W / 1 I count_mismatch, high_contamination, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD010820 | O-GlcNAcylation enhances double strand break repair, promotes cancer cell proliferation and prevents therapy-induced senescence in irradiated tumors | Homo sapiens | none | 12 | 259,817 | 3,369 | 16,115 | 0 E / 5 W / 1 I count_mismatch, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD011314 | Profiling of Methylglyoxal Blood Metabolism and Advanced Glycation End-Product Proteome using a Chemical Probe | Homo sapiens | chemical_probe | 17 | 4,868 | 57 | 580 | 0 E / 7 W / 1 I calibration_failed, high_contamination, low_core_use, low_id_rate, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD011740 | Translational regulation contributes to the secretory response of chondrocytic cells following exposure to Interleukin-1B | Homo sapiens | none | 12 | 89,011 | 2,112 | 6,207 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites, unresolved_modifications |
| PXD012213 | Effects of Caloric Restriction with Protein Supplementation on Plasma Protein Profiles in Middle-Aged Women with Metabolic Syndrome – A Preliminary Open Study | Homo sapiens | none | 26 | 193,217 | 320 | 4,786 | 0 E / 4 W / 1 I count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD012307 | An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics | Mus musculus | none | 32 | 2,067,679 | 7,801 | 95,871 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, occupancy_decoy_groups, occupancy_not_stored, sdrf_conflicting_rows, sdrf_uncoded, unplaced_ptm_sites |
| PXD012753 | Young, old, OVX mouse Skin LC-MSMS, 3M Urea extraction | Mus musculus | none | 15 | 43,949 | 1,032 | 2,912 | 0 E / 7 W / 1 I high_contamination, low_core_use, low_id_rate, mbr_kept_exceeds_msms, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD012754 | Ageing Mouse Skin LC-MSMS, NaCl extraction | Mus musculus | none | 10 | 11,842 | 780 | 2,140 | 0 E / 8 W / 0 I calibration_failed, high_contamination, low_core_use, low_id_rate, mbr_kept_exceeds_msms, no_sdrf, occupancy_not_stored, unplaced_ptm_sites |
| PXD013240 | Intracellular proteome (SDS/Na-DoC) extract from EP/LP MSCs grown on soft/stiff hydrogels for 4 days | Homo sapiens | none | 16 | 132,407 | 2,806 | 9,315 | 0 E / 4 W / 1 I high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD013640 | Keap-1-mediated S-nitrosylation of NOX4 hampers oxidative damage in endothelium | Homo sapiens | chemical_probe | 16 | 56,309 | 793 | 2,856 | 0 E / 6 W / 1 I count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD014097 | Auto-phosphorylation at serine 166 regulates RIP kinase 1 mediated cell death and inflammation | Mus musculus | phospho | 12 | 150,342 | 4,072 | 19,650 | 0 E / 6 W / 1 I count_mismatch, cysteine_poor, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD014098 | CLUH-dependent RNA granules coordinate mitochondrial catabolic pathways with mTORC1 signaling and mitophagy | Mus musculus | none | 16 | 1,040,626 | 4,933 | 32,132 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD014274 | Proteomic and unbiased post-translational modification profiling of amyloid plaques and surrounding tissue in a transgenic mouse model of Alzheimer’s disease | Mus musculus | none | 38 | 116,639 | 1,318 | 7,280 | 0 E / 8 W / 5 I 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 |
| PXD014416 | Spatiotemporal proteomics of hormone treated mice (urine across time, prostate tissue) | Mus musculus | none | 47 | 594,741 | 4,960 | 26,873 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD015079 | Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix | Homo sapiens | none | 12 | 261,188 | 2,689 | 11,932 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, cysteine_poor, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD015170 | The GID Ubiquitin Ligase Complex is a Regulator of AMPK Activity and Organismal Lifespan | Mus musculus | none | 18 | 121,033 | 2,744 | 4,189 | 0 E / 5 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD015239 | Epigenetic contributions to hemisphere asymmetry in healthy brain, aging, and Parkinson’s disease | Homo sapiens | none | 10 | 229,035 | 2,140 | 8,495 | 0 E / 5 W / 1 I count_mismatch, cysteine_poor, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD015729 | Murine hippocampus after radiation LC-MSMS | Mus musculus | none | 16 | 319,370 | 3,051 | 12,871 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD016430 | MiR-29 coordinates age-dependent plasticity brakes in the adult visual cortex | Mus musculus | none | 44 | 759,941 | 3,715 | 8,882 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD016793 | Proteomics analysis of rat liver after disulfiram treatment | Rattus norvegicus | none | 24 | 2,314,854 | 5,609 | 42,538 | 0 E / 6 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, unplaced_ptm_sites |
| PXD017058 | Astrocyte Support for Oligodendrocyte Differentiation can be Conveyed via Extracellular Vesicles but Diminishes with Age | Mus musculus | none | 9 | 182,903 | 2,419 | 19,068 | 0 E / 6 W / 1 I count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD017475 | The lncRNA MIR31HG regulates the senescence associated secretory phenotype | Homo sapiens | affinity_purification | 19 | 187,253 | 2,277 | 17,751 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD017505 | Autofluorescence positive and negative microglia constitute novel subsets found in healthy brain. | Mus musculus | none | 17 | 522,900 | 4,078 | 17,913 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD017944 | Proteomic analysis of scleraxis mutant tendon | Mus musculus | none | 20 | 69,785 | 879 | 5,405 | 0 E / 5 W / 1 I high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD018097 | YME1L1 KnockOut MEF Cells Whole Proteomics | Mus musculus | phospho (on some runs only; runs differ) | 12 | 762,720 | 8,079 | 52,657 | 0 E / 7 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, mixed_enrichment, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, spectral_library, unplaced_ptm_sites |
| PXD018315 | Identification of proteins that interact with the lncRNA Sarrah | Mus musculus | affinity_purification | 40 | 79,679 | 1,442 | 5,147 | 0 E / 4 W / 2 I collapsed_duplicate_rows, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD018399 | Reduced proteasome activity in the aging brainresults in ribosome stoichiometry loss and aggregation | Mus musculus | other (on some runs only; runs differ) | 20 | 161,098 | 3,380 | 5,953 | 0 E / 6 W / 1 I count_mismatch, low_core_use, mixed_enrichment, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD018545 | Endoplasmic Reticulum Stress-mediated Mitochondrial Dysfunction in Aged Hearts | Mus musculus | none | 18 | 316,110 | 1,037 | 7,211 | 0 E / 5 W / 1 I count_mismatch, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD018655 | Proteomic analysis of small extracellular vesicles derived from human ESCs | Homo sapiens | none | 15 | 201,398 | 4,334 | 16,354 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD018969 | Keap1 governs ageing-induced protein aggregation in endothelial cells | Homo sapiens | none | 19 | 220,119 | 2,966 | 4,903 | 0 E / 7 W / 3 I 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 |
| PXD018999 | A dichotomous response to chronic fetal hypoxia preprograms aging already during kidney development | Mus musculus | none | 48 | 974,746 | 8,239 | 46,440 | 0 E / 8 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, spectral_library, unplaced_ptm_sites |
| PXD019279 | Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss | Homo sapiens | none | 51 | 1,665,837 | 5,256 | 46,224 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD019849 | Nerv. System Specific Yme1l KO (NYKO) Mice Retina Samples (30-31wks old) | Mus musculus | none | 10 | 668,514 | 5,975 | 30,700 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD020462 | Oxidative damage signatures in human bone collagen from Pompeii and Herculaneum. | Homo sapiens | none | 15 | 4,035 | 46 | 448 | 0 E / 7 W / 1 I calibration_failed, cysteine_poor, high_contamination, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, peptide_rows_localization_ambiguous |
| PXD021069 | Matrix reverses immortalization-mediated stem cell fate determination | Homo sapiens | none | 14 | 186,914 | 1,349 | 3,052 | 0 E / 6 W / 1 I count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD021762 | Mitochondrial mistranslation is modulated by metabolic stress | Mus musculus | other | 33 | 227,290 | 1,586 | 8,307 | 0 E / 5 W / 1 I count_mismatch, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD022128 | A genome-wide screen for essentiality upon telomerase inhibition identifies a novel p53 regulator, C16ORF72/TAPR1 | Homo sapiens | proximity_labelling | 18 | 38,855 | 1,280 | 1,412 | 0 E / 5 W / 1 I low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD022180 | Mytho, An Uncharacterized Gene that Controls Longevity and WIPI2-dependent Autophagy | Homo sapiens | immunoprecipitation | 18 | 118,902 | 1,853 | 9,342 | 0 E / 6 W / 2 I calibration_failed, collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD022196 | Chaperone-mediated autophagy sustains hematopoietic stem cell function | Mus musculus | none | 32 | 250,902 | 3,800 | 13,517 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, low_id_rate, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD022227 | Col4a5 mouse glomerular extracellular matrix | Mus musculus | none | 35 | 184,016 | 2,876 | 9,756 | 0 E / 6 W / 1 I high_contamination, low_core_use, mbr_kept_exceeds_msms, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD022363 | Col4a1 mouse glomerular datasets | Mus musculus | none | 12 | 56,170 | 1,565 | 4,726 | 0 E / 5 W / 1 I high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD022393 | Circadian Regulation of Protein Cargo in Exosomes | Mus musculus | none | 54 | 127,036 | 1,823 | 7,264 | 0 E / 7 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD022678 | The landscape of molecular chaperones across human tissues reveals a layered architecture of core-variable chaperones | Mus musculus | none | 9 | 735,560 | 5,887 | 47,742 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD022737 | proteomic changes in aging rats treated with the cognitive enhancer CE-123 | Rattus norvegicus | other | 24 | 627,316 | 4,672 | 33,594 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD023381 | Transcriptional and proteomic characterization of telomere-induced senescence in a human alveolar epithelial cell line | Homo sapiens | affinity_purification | 20 | 42,734 | 1,278 | 5,335 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD024216 | Shotgun-based Proteomics of Extracellular Vesicles in Alzheimer’s Disease Reveals Biomarkers Involved in Immunological and Coagulation Pathways | Homo sapiens | none | 57 | 181,016 | 1,260 | 4,438 | 0 E / 5 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD024478 | RNA polymerase I transcription disturbances lead to instable ribosomes in Cockayne syndrome | Homo sapiens | none | 20 | 469,358 | 7,044 | 32,060 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, spectral_library, unplaced_ptm_sites |
| PXD024633 | Mitochondrial mistranslation modulated by metabolic stress causes cardiovascular disease and reduced life-span | Mus musculus | none | 10 | 667,123 | 3,006 | 14,203 | 0 E / 5 W / 1 I count_mismatch, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, sdrf_uncoded, unplaced_ptm_sites |
| PXD024685 | Proteomic analyses of non-preconditioned murine kidneys pre- and post-IRI in comparison to kidneys after preconditioning by hypoxia or caloric restriction | Mus musculus | none | 30 | 835,173 | 4,821 | 21,618 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD024803 | CHD6 IP from human induced pluripotent stem cells LC-MS-MS | Homo sapiens | immunoprecipitation | 28 | 381,202 | 2,202 | 19,715 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD025240 | Hippocampal disruptions of synaptic and astrocyte metabolism during early amyloid pathology in the 5xFAD mouse model of Alzheimer’s disease | Mus musculus | none | 32 | 3,136,315 | 6,942 | 39,456 | 0 E / 6 W / 1 I count_mismatch, low_core_use, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, sdrf_uncoded, unplaced_ptm_sites |
| PXD025280 | Early- and late-passage primary human mesemchymal stem cells subjected to 2 hour heat shock | Homo sapiens | none | 16 | 214,292 | 3,273 | 8,453 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD025321 | Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia | Mus musculus | none | 15 | 771,808 | 4,351 | 27,803 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD025503 | Obesity causes irreversible mitochondria failure in visceral adipose tissue despite successful anti-obesogenic lifestyle | Mus musculus | none | 9 | 521,289 | 4,656 | 34,371 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD026219 | Training-induced bioenergetic improvement in human skeletal muscle is associated with non-stoichiometric changes in the mitochondrial proteome without reorganisation of respiratory chain content | Homo sapiens | none | 41 | 632,869 | 2,555 | 21,985 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD026335 | Mouse Heart SS-31 Proteome and Phosphoproteome | Mus musculus | none | 20 | 940,017 | 3,805 | 51,105 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD026608 | Integrated analysis of proteomics and phosphoproteomics on rat hearts with aging and hypertension | Rattus norvegicus | phospho | 12 | 266,155 | 2,467 | 14,322 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD026934 | Mitochondria regulate dietary lipid processing in enterocytes | Mus musculus | none | 20 | 904,188 | 7,573 | 24,351 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD027318 | Identification of a Proteomic Signature of Senescence in Primary Human Mammary Epithelial Cells | Homo sapiens | none | 18 | 378,168 | 4,478 | 21,704 | 0 E / 6 W / 3 I collapsed_duplicate_rows, count_mismatch, no_design_file, no_output_sdrf, no_sdrf, occupancy_decoy_groups, unplaced_ptm_sites, upstream_provenance_changed |
| PXD027526 | Mapping sites of carboxymethyllysine modification on proteins reveals consequences for proteostasis and cell proliferati | Mus musculus | none | 153 | 643,119 | 6,953 | 23,757 | 0 E / 7 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, unplaced_ptm_sites |
| PXD027734 | Proximity-biotinylation (BioID) to dissect cytoplasmic p53 signaling networks under nutrient stress | Homo sapiens | proximity_labelling | 19 | 487,237 | 5,374 | 24,722 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD027754 | Metabolic reprogramming during hyperammonemia targets mitochondrial function and post-mitotic senescence | Rattus norvegicus | none | 20 | 116,756 | 487 | 2,532 | 0 E / 6 W / 1 I count_mismatch, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD027971 | Simple, single-shot phosphoproteomic analysis of heat-stable tau | Rattus norvegicus | phospho | 15 | 247,005 | 1,184 | 16,641 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, cysteine_poor, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD028157 | Proteomics quantification of striatal fraction from DAT-KO and WT rats | Rattus norvegicus | none | 20 | 1,351,827 | 5,126 | 43,069 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD028590 | Amphiregulin mediates non-cell-autonomous effect of senescence on reprogramming | Mus musculus | none | 24 | 487,235 | 2,560 | 34,170 | 0 E / 5 W / 1 I count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD028852 | Proteins enriched on damaged lysosomes in 293T | Homo sapiens | proximity_labelling | 20 | 88,611 | 2,823 | 8,248 | 0 E / 5 W / 1 I high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD028865 | Unbiased in vivo exploration of nuclear bodies-enhanced sumoylation reveals that PML orchestrates embryonic stem cell fa | Mus musculus | affinity_purification | 32 | 1,028,186 | 3,179 | 30,774 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD028975 | Engineering Extracellular Vesicles by Three-dimensional Dynamic Culture of Human Mesenchymal Stem Cells | Homo sapiens | none | 30 | 563,284 | 2,055 | 18,331 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, spectral_library, unplaced_ptm_sites |
| PXD029116 | Articular cartilage proteome differentiates by zones during osteoarthritis | Homo sapiens | none | 30 | 66,215 | 402 | 3,896 | 0 E / 4 W / 1 I low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD030773 | The proto-oncogene TCL1A deregulates mitotic checkpoint transition and genomic stability in CLL | Homo sapiens | none | 30 | 847,058 | 5,942 | 35,306 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD030776 | The proto-oncogene TCL1A deregulates mitotic checkpoint transition and genomic stability in CLL | Homo sapiens | immunoprecipitation | 12 | 139,095 | 2,111 | 7,684 | 0 E / 6 W / 1 I count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD030939 | A compound-based therapy approach for epidermolysis bullosa simplex (EBS) | Homo sapiens | phospho (on some runs only; runs differ) | 20 | 1,169,720 | 7,958 | 75,247 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, mixed_enrichment, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD031223 | Chronic Aicar Treatment Identifies Sex-specific Phenotypes in the Aging Mouse Heart | Mus musculus | none | 8 | 125,466 | 1,324 | 2,326 | 0 E / 6 W / 1 I count_mismatch, cysteine_poor, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD031604 | Analysis of 20-HETE supplementation in calorically restricted C57Bl6 mice | Mus musculus | none | 15 | 1,406,442 | 6,865 | 55,041 | 0 E / 6 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, unplaced_ptm_sites |
| PXD032040 | Translational specialization in pluripotency by RBPMS poises future lineage-decisions | Homo sapiens | immunoprecipitation | 15 | 118,909 | 2,538 | 9,604 | 0 E / 7 W / 3 I 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 |
| PXD032044 | Characterization of the skeletal muscle proteome in under-nourished old rats | Rattus norvegicus | none | 44 | 871,294 | 3,003 | 31,761 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD032046 | Translational specialization in pluripotency by RBPMS poises future lineage-decisions | Homo sapiens | none | 12 | 144,907 | 3,751 | 6,003 | 0 E / 4 W / 2 I collapsed_duplicate_rows, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD032202 | Global and comparative proteome signatures in the lens capsule, trabecular meshwork, and iris of patients with pseudoexfoliation glaucoma | Homo sapiens | none | 21 | 183,023 | 1,925 | 14,088 | 0 E / 5 W / 2 I count_mismatch, no_design_file, no_output_sdrf, no_sdrf, occupancy_decoy_groups, unplaced_ptm_sites, upstream_provenance_changed |
| PXD032240 | Unbiased in vivo exploration of nuclear bodies-enhanced sumoylation reveals that PML orchestrates embryonic stem cell fa | Mus musculus | affinity_purification | 24 | 375,188 | 3,131 | 25,201 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD032757 | The role of extracellular vesicles in synovial fibroblast senescence | Homo sapiens | none | 11 | 66,715 | 1,400 | 6,320 | 0 E / 6 W / 1 I count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD033430 | Dysregulated cellular redox status during hyperammonemia causes mitochondrial dysfunction by inhibiting sirtuin mediated | Mus musculus | acetyl | 9 | 29,476 | 1,318 | 2,817 | 0 E / 5 W / 1 I low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD034432 | Tracking prostate carcinogenesis over time through urine proteome profiling in an animal model: an exploratory approach | Rattus norvegicus | none | 10 | 38,154 | 608 | 3,363 | 0 E / 7 W / 1 I count_mismatch, high_contamination, low_core_use, low_id_rate, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD034465 | Surface proteome profiling of p53-restorable murine liver cancer cells | Mus musculus | affinity_purification | 19 | 669,101 | 4,844 | 22,231 | 0 E / 6 W / 1 I count_mismatch, cysteine_poor, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD034590 | Profiling of purified autophagic vesicle content and degradome in the maturing and aging brain | Mus musculus | affinity_purification | 81 | 2,574,920 | 6,467 | 43,185 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, occupancy_decoy_groups, occupancy_not_stored, sdrf_partial, sdrf_uncoded, unplaced_ptm_sites |
| PXD035107 | Global phosphoproteomic profiling of skeletal muscle in ovarian-hormone deficient mice | Mus musculus | phospho | 8 | 69,974 | 1,442 | 11,612 | 0 E / 6 W / 1 I count_mismatch, cysteine_poor, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD035149 | ORP6 regulates astrocytic cholesterol metabolism and brain Aβ deposition | Mus musculus | none | 20 | 763,140 | 3,088 | 25,314 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD035171 | Natural aging and ovariectomy induces parallel phosphoproteomic alterations in skeletal muscle of female mice | Mus musculus | phospho | 14 | 223,143 | 1,887 | 16,884 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, cysteine_poor, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD035299 | Nuclear protein expression profiling of IMR90 RAS cells compared to IMR90 Control cells | Homo sapiens | other | 10 | 1,174,457 | 5,677 | 37,575 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, spectral_library, unplaced_ptm_sites |
| PXD035412 | Proteomics analysis of tissue aging nucleic acid binding proteins | Homo sapiens | phospho | 30 | 1,268,270 | 6,955 | 64,817 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD035446 | Extracellular vesicle-derived miRNAs improve stem cell-based therapeutic approaches in muscle wasting conditions. | Mus musculus | none | 12 | 19,796 | 235 | 1,169 | 0 E / 6 W / 1 I high_contamination, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD036557 | Modelling Premature Cardiac Aging with Induced Pluripotent Stem Cells From a Hutchinson-Gilford Progeria Syndrome Patient | Homo sapiens | none | 18 | 26,582 | 1,652 | 2,091 | 0 E / 6 W / 2 I high_contamination, low_id_rate, no_design_file, no_output_sdrf, occupancy_decoy_groups, sdrf_skeleton, unplaced_ptm_sites, upstream_provenance_changed |
| PXD037230 | Scleraxis-lineage cells are required for tendon homeostasis and their depletion induces an accelerated extracellular mat | Mus musculus | none | 12 | 303,336 | 2,283 | 9,419 | 0 E / 5 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD038328 | Organ protection by caloric restriction depends on activation of the de novo NAD+ synthesis pathway | Mus musculus | acetyl (on some runs only; runs differ) | 40 | 1,397,244 | 4,719 | 48,143 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, mixed_enrichment, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD038718 | An NPAS4:NuA4 complex couples synaptic activity to DNA repair | Mus musculus | immunoprecipitation | 14 | 40,677 | 1,754 | 2,256 | 0 E / 7 W / 1 I cysteine_poor, high_contamination, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD039172 | Proteome of the cortex of old Pink1-SNCA A53T double mutant Parkinson mice | Mus musculus | none | 98 | 1,033,275 | 6,671 | 41,458 | 0 E / 6 W / 2 I calibration_failed, collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD041139 | Proteomic analysis reveals insufficient folliculogenesis in Aging Female associates with infertility | Homo sapiens | none | 14 | 432,972 | 492 | 10,811 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD041376 | Profiling of purified autophagic vesicle content and degradome in the maturing and aging brain - Part II | Mus musculus | none | 20 | 1,665,643 | 6,181 | 25,872 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD041660 | A Defective Extracellular Matrix/Kindlin-2/Actin/ERK Mechanosensing Pathway Affects Fibroblast-To-Myofibroblast Transiti | Mus musculus | none | 8 | 122,316 | 1,224 | 2,428 | 0 E / 6 W / 1 I count_mismatch, cysteine_poor, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD041766 | Remodeling of the focal adhesion complex by hydrogen-peroxide- induced senescence | Mus musculus | none | 8 | 199,344 | 3,372 | 23,381 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD042301 | Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process. | Mus musculus | proximity_labelling | 31 | 363,181 | 3,712 | 12,533 | 0 E / 4 W / 3 I collapsed_duplicate_rows, contaminant_label_unresolved, high_contamination, no_design_file, no_output_sdrf, occupancy_decoy_groups, unplaced_ptm_sites |
| PXD043001 | Proteomic characterizationof the circle of Willis during aging | Mus musculus | none | 40 | 2,821,853 | 8,548 | 60,348 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD043644 | Liver-derived plasminogen mediates muscle stem cell expansion during caloric restriction through the plasminogen recepto | Mus musculus | none | 12 | 88,987 | 399 | 2,268 | 0 E / 5 W / 1 I high_contamination, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored |
| PXD043779 | Evaluation of the secretome of senescent melanoma cells and the impact of silencing Mfn1 on the senescence-associated se | Mus musculus | none | 24 | 272,721 | 2,378 | 11,337 | 0 E / 6 W / 1 I count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD043964 | Luminal cerebrovascular proteomic changes during aging | Mus musculus | affinity_purification | 12 | 32,392 | 919 | 3,711 | 0 E / 6 W / 1 I high_contamination, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD044227 | Food perception liver phosphoproteome induced by caged food and POMC neuron activation | Mus musculus | phospho | 61 | 457,219 | 4,506 | 23,252 | 0 E / 6 W / 1 I count_mismatch, cysteine_poor, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, spectral_library, unplaced_ptm_sites |
| PXD044453 | Age-Dependent Effects of Voluntary Exercise on Urinary Voiding Function and Frailty-Related Metrics in Mice | Mus musculus | none | 40 | 164,088 | 350 | 4,896 | 0 E / 6 W / 1 I count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD044773 | Cell-specific crosstalk proteomics reveals cathepsin B signaling as a driver of glioblastoma malignancy near the subventricular zone | Homo sapiens | none | 21 | 423,041 | 3,645 | 21,783 | 0 E / 8 W / 2 I 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 |
| PXD044996 | LC-MS/MS analysis of isolated murine brain endothelial cells (BECs) from 3-, 6-, 12-, and 18-months-old mice and Apoe-KO | Mus musculus | none | 25 | 285,043 | 4,166 | 17,804 | 0 E / 9 W / 2 I 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 |
| PXD045821 | Intracellular Iron Accumulation Facilitates Mycobacterial Infection in Old Mouse Macrophages | Mus musculus | none | 12 | 230,387 | 3,089 | 8,220 | 0 E / 6 W / 1 I count_mismatch, high_contamination, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD045861 | Myelin-axon interface disruption uncovered by subcellular proteomics and imaging of Alzheimer’s human brain | Homo sapiens | proximity_labelling | 20 | 312,904 | 2,682 | 10,588 | 0 E / 9 W / 1 I 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 |
| PXD045887 | An Intra-Individual Paired Mass Spectrometry dataset for decoding Solar-Induced Proteomic Changes in Facial Skin | Homo sapiens | none | 40 | 416,021 | 1,164 | 6,098 | 0 E / 5 W / 2 I collapsed_duplicate_rows, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD047288 | Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain | Rattus norvegicus | affinity_purification | 36 | 8,398 | 367 | 1,602 | 0 E / 6 W / 1 I cysteine_poor, high_contamination, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD047289 | Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain | Rattus norvegicus | affinity_purification | 22 | 37,693 | 1,035 | 2,493 | 0 E / 6 W / 1 I count_mismatch, cysteine_poor, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD047292 | Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain | Rattus norvegicus | affinity_purification | 36 | 10,059 | 240 | 1,568 | 0 E / 5 W / 1 I cysteine_poor, low_id_rate, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD047293 | Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain | Rattus norvegicus | affinity_purification | 34 | 28,664 | 486 | 2,039 | 0 E / 8 W / 3 I 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 |
| PXD048393 | Acetyl-CoA Carboxylase Obstructs CD8+ T-Cell Lipid Utilization in the Tumor Microenvironment | Mus musculus | none | 15 | 1,524,774 | 6,589 | 56,007 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD048720 | Proteomic analysis of a rat streptozotocin model shows dysregulated biological pathways implicated in Alzheimer’s Disease | Rattus norvegicus | none | 29 | 1,325,918 | 4,202 | 29,907 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD048877 | Egr1 is a master regulator of regenerative senescence and cardiac repair | Mus musculus | none | 30 | 1,804,710 | 4,864 | 37,379 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD049018 | BJ cyto-nuclear translocation upon STING activation | Homo sapiens | proximity_labelling | 20 | 104,625 | 1,626 | 10,007 | 0 E / 6 W / 1 I count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, spectral_library, unplaced_ptm_sites |
| PXD049957 | Phosphoproteomics of consecuively active AKT in liver and Insulin stimulated primary Hepatocytes | Mus musculus | phospho | 34 | 1,864,731 | 7,308 | 55,541 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD050351 | Targeting upstream Hippo-pathway kinases releases the scaffolder WWC1 to promote synaptic plasticity and long-term memory in mice | Homo sapiens | chemical_probe | 20 | 213,526 | 1,481 | 7,765 | 0 E / 4 W / 2 I collapsed_duplicate_rows, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD051203 | Protein degradation targets in the retrosplenial cortex of the female aged brain | Rattus norvegicus | affinity_purification | 39 | 34,103 | 921 | 2,133 | 0 E / 6 W / 2 I cysteine_poor, excluded_from_search, high_contamination, low_id_rate, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD051644 | Protein degradation targets in hippocampus of the aged brain following context exposure | Rattus norvegicus | affinity_purification | 23 | 23,705 | 537 | 1,678 | 0 E / 7 W / 2 I cysteine_poor, excluded_from_search, high_contamination, low_core_use, low_id_rate, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD051715 | Age-related proteostatic imbalance exacerbates heart failure with preserved ejection fraction pathogenesis in old mice | Mus musculus | none | 21 | 1,742,303 | 3,377 | 45,521 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD052189 | Microglial-derived C1q integrates into neuronal ribonucleoprotein complexes and impacts protein homeostasis in the aging | Mus musculus | immunoprecipitation | 32 | 15,718 | 577 | 1,456 | 0 E / 8 W / 2 I 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 |
| PXD052631 | G-CSF/NAMPT signaling drives neutrophil dysfunction and enhances bacterial infection susceptibility in cancer patients | Mus musculus | none | 22 | 41,561 | 1,003 | 3,303 | 0 E / 7 W / 1 I count_mismatch, high_contamination, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD052797 | Increased levels of extracellular matrix proteins in extracellular vesicles from brains of aged mice. | Mus musculus | none | 54 | 416,306 | 1,591 | 9,068 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD053288 | RyR2-mediated calcium leak increases glyoxalase I in the aging brain | Mus musculus | none | 12 | 660,574 | 4,947 | 33,379 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, cysteine_poor, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD054290 | Mouse bone marrow-derived macrophages (BMDMs) loaded with atherogenic LDL | Mus musculus | none | 20 | 1,403,775 | 4,144 | 26,926 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD055228 | GPC3-mediated metabolic rewiring of diabetic mesenchymal stromal cells enhances their cardioprotective functions via pyr | Mus musculus | immunoprecipitation | 15 | 2,687 | 130 | 267 | 0 E / 7 W / 1 I high_contamination, low_core_use, low_id_rate, mbr_kept_exceeds_msms, occupancy_decoy_groups, occupancy_not_stored, sdrf_partial, sdrf_uncoded |
| PXD056276 | SORLA upregulation suppresses global pathological effects in aged tauopathy mouse brain | Mus musculus | none | 26 | 961,245 | 3,959 | 13,265 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD056433 | M1 polyubiquitin targets in the hippocampus of young and aged male rats following contextual fear conditioning | Rattus norvegicus | other | 40 | 77,681 | 240 | 1,669 | 0 E / 6 W / 1 I cysteine_poor, low_core_use, low_id_rate, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD056458 | M1 polyubiquitin targets in the hippocampus across the lifespan | Rattus norvegicus | affinity_purification | 38 | 118,038 | 357 | 1,962 | 0 E / 4 W / 1 I cysteine_poor, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD057407 | Proteomic and Phosphoproteomic Signatures of Aging Mouse Liver | Mus musculus | none | 10 | 921,483 | 4,258 | 16,734 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD057409 | Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease_C2C12 myotube p | Mus musculus | none | 9 | 484,238 | 4,053 | 18,842 | 0 E / 4 W / 1 I count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD057490 | Synaptic phosphoproteome modifications and cortical circuit dysfunction are linked to the early-stage progression of alpha-synuclein pathology | Rattus norvegicus | phospho | 8 | 93,079 | 1,944 | 9,155 | 0 E / 6 W / 1 I count_mismatch, cysteine_poor, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD057499 | Synaptic phosphoproteome modifications and cortical circuit dysfunction are linked to the early-stage progression of alpha-synuclein pathology | Rattus norvegicus | none | 8 | 249,655 | 2,865 | 6,985 | 0 E / 5 W / 1 I count_mismatch, cysteine_poor, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD057502 | Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease-C2C12 myotube p | Mus musculus | phospho | 9 | 82,421 | 2,085 | 7,777 | 0 E / 6 W / 1 I count_mismatch, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD057544 | Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease- C2C12 myotube | Mus musculus | acetyl | 9 | 26,740 | 1,223 | 2,489 | 0 E / 5 W / 1 I low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD057545 | Chaperone-mediated autophagy sex-specifically regulates neuronal activity by remodeling the synaptic proteome | Mus musculus | none | 24 | 625,331 | 3,627 | 13,507 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD057554 | Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease-Mouse skeletal | Mus musculus | none | 8 | 69,522 | 720 | 2,646 | 0 E / 7 W / 1 I count_mismatch, high_contamination, low_core_use, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD058082 | Major toxin composition of particulate matter from a coal-fired power plant and its proteomics-associated toxicological | Mus musculus | none | 15 | 42,223 | 1,203 | 1,820 | 0 E / 5 W / 1 I collapsed_duplicate_rows, low_core_use, low_id_rate, no_sdrf, occupancy_not_stored, unplaced_ptm_sites |
| PXD058156 | Temozolomide Induces Glioblastoma Dedifferentiation into Highly Malignant Stem-like Cells Through Senescence-Associated Reprogramming via HIF1α/HIF2α Regulation | Homo sapiens | none | 12 | 1,049,383 | 7,570 | 40,180 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, spectral_library, unplaced_ptm_sites |
| PXD058248 | K63 polyubiquitin targets in the hippocampus across the lifespan | Rattus norvegicus | affinity_purification | 38 | 43,066 | 239 | 1,955 | 0 E / 4 W / 1 I low_id_rate, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD058253 | K63 polyubiquitin targets in the amygdala across the lifespan | Rattus norvegicus | affinity_purification | 38 | 12,726 | 139 | 1,541 | 0 E / 6 W / 1 I count_mismatch, low_core_use, low_id_rate, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD058611 | Enhanced non-enzymatic H2S generation extends lifespan and healthspan in male mice | Mus musculus | none | 15 | 194,800 | 2,126 | 6,146 | 0 E / 5 W / 1 I count_mismatch, cysteine_poor, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD058775 | DNA Damage in Macrophages Drives Immune Autoreactivity via Nuclear Antigen Presentation | Mus musculus | immunoprecipitation | 18 | 1,859 | 153 | 128 | 0 E / 6 W / 1 I calibration_failed, contaminant_label_unresolved, high_contamination, low_id_rate, no_design_file, no_output_sdrf, no_sdrf |
| PXD058855 | KAT5-mediated acetylation of PC4 facilitates DNA repair by promoting chromatin reorganization | Homo sapiens | affinity_purification | 25 | 78,573 | 1,083 | 4,120 | 0 E / 6 W / 1 I count_mismatch, high_contamination, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD058971 | Multi-omics Analysis Shed Light on the Extracellular Role of PCMT1 | Mus musculus | none | 32 | 1,549,119 | 9,704 | 39,912 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD059520 | 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 | Rattus norvegicus | none | 21 | 162,200 | 1,681 | 5,807 | 0 E / 5 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD059818 | Simultaneous profiling of native-state proteomes and transcriptomes of brain cell types using proximity labeling | Mus musculus | proximity_labelling | 38 | 505,085 | 4,439 | 20,174 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD060832 | Mitochondrial regulator PGC-1a in neuronal metabolism and brain aging | Mus musculus | none | 15 | 151,455 | 1,746 | 5,137 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD060982 | mTOR orchestrates sequential phases of ependymal cell differentiation by acting on their alternative cell cycle and cent | Mus musculus | phospho | 8 | 327,734 | 6,060 | 49,503 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD061069 | The SET1/COMPASS subunit RBBP5 orchestrates epigenetic control of global proteostasis and the 12h oscillator to safeguar | Mus musculus | proximity_labelling | 120 | 586,221 | 3,220 | 15,631 | 0 E / 8 W / 1 I 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 |
| PXD061654 | The mammalian longevity associated acetylome | Mus musculus | acetyl (on some runs only; runs differ) | 30 | 2,789,721 | 3,866 | 36,045 | 0 E / 6 W / 1 I count_mismatch, mixed_enrichment, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, unplaced_ptm_sites |
| PXD064236 | DLX2-FLAG IP-MS in embryonic bodies (EBs): Protein complexes identification | Mus musculus | immunoprecipitation | 16 | 25,389 | 509 | 2,336 | 0 E / 7 W / 1 I count_mismatch, cysteine_poor, high_contamination, low_id_rate, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD067102 | Young and aged T cells LC-MS/MS | Mus musculus | none | 12 | 1,510,240 | 5,016 | 45,258 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD067622 | DNA-Protein Crosslinks Promote cGAS-STING-driven Premature Aging and Embryonic Lethality | Homo sapiens | proximity_labelling | 24 | 623,207 | 4,167 | 21,493 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD068498 | Reduced IGF-1 signaling fails to limit Alzheimer’s disease progression in a novel rat model of IGF-1R haploinsufficiency | Rattus norvegicus | none | 47 | 1,143,559 | 3,969 | 25,440 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD069093 | Kinome profiling of osteosarcoma patient-derived xenograft TT2 treated with palbociclib | Homo sapiens | affinity_purification | 16 | 490,676 | 2,078 | 15,824 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, occupancy_decoy_groups, occupancy_not_stored, sdrf_skeleton, unplaced_ptm_sites |
| PXD071171 | Mitochondrial IntegrityMitochondrial Integrity Modulates mTOR Signaling and Podocyte Function Modulates mTOR Signaling and Podocyte Function | Mus musculus | phospho | 20 | 662,717 | 7,785 | 56,740 | 0 E / 4 W / 2 I collapsed_duplicate_rows, count_mismatch, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD073846 | mtDNA alterations determine myoblast differentiation and disrupt skeletal muscle architecture | Mus musculus | proximity_labelling | 12 | 171,140 | 2,307 | 9,019 | 0 E / 6 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, low_core_use, occupancy_decoy_groups, occupancy_not_stored, sdrf_uncoded, unplaced_ptm_sites |
| PXD073999 | Mechanisms of the antiproliferative effects of SIRT6 inhibition in melanoma: A multi-omics analysis | Homo sapiens | none | 12 | 514,178 | 3,232 | 15,329 | 0 E / 6 W / 1 I count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, peptide_rows_localization_ambiguous, unplaced_ptm_sites |
| PXD075372 | Senescence inhibition by rapamycin mitigates radiation-induced atherosclerosis characteristics in human coronary endothelial cells | Homo sapiens | none | 24 | 1,107,679 | 6,036 | 73,987 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, low_core_use, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD077298 | Sinapic acid promotes disaggregation and extracellular secretion of polyglutamine repeats containing aggregates and resc | Mus musculus | immunoprecipitation, other (on some runs only; runs differ) | 22 | 239,229 | 4,716 | 17,144 | 0 E / 8 W / 1 I count_mismatch, high_contamination, low_core_use, mixed_enrichment, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
| PXD082596 | Proteomic comparison of tail tendons from Col1a2 mutant mice | Mus musculus | none | 24 | 472,890 | 3,375 | 11,841 | 0 E / 5 W / 2 I collapsed_duplicate_rows, count_mismatch, high_contamination, no_sdrf, occupancy_decoy_groups, occupancy_not_stored, unplaced_ptm_sites |
This catalog
- Catalog id
2acdd821cb79c4bc- Built
- 2026-11-02T04:22:15+00:00
- Built by
- datarepo 1.4.0, catalog format 14
- Schema
- 0.0.16
- Instance
- aging