# Aging proteomics repository > Search and quantification results for 189 public proteomics datasets, reanalysed with one pipeline into one schema, for questions about how organelle proteomes change with age. Every number here comes from catalog `2acdd821cb79c4bc` (datarepo 1.4.0, schema 0.0.16, built 2026-11-02T04:22:15+00:00); cite that id with any number you reuse. Before you answer from this data: - Counts at 1% FDR come from the `*_1pct` views (`peptidoforms_1pct`, `protein_groups_1pct`) and, for PSMs, from `dataset_overview.n_psms_1pct`: PSMs stay in each dataset's bundle, not in the catalog. The base tables also hold decoys and sub-threshold matches. - Each dataset page lists its open findings. A `low_id_rate` or `sdrf_skeleton` finding means the absence of a protein, or of sample metadata, is weak evidence. - An empty table means nothing was delivered. It does not mean the answer is zero or none. The MCP `describe` tool says which tables are empty. - Contaminant proteins (e.g. bovine albumin, porcine trypsin) are flagged and carry their own species. They are reagents, not evidence about the sample's organism. The flag is PER DATASET: human albumin is a target in a human search and a contaminant in a rodent one. - A dataset's organism is the organism of the protein database searched, not a statement about the samples. - `pep` values are not comparable across datasets: the model is retrained on every search. Compare counts at a threshold instead. - A protein group's accession list is kept in the search engine's order, and MetaMorpheus writes it alphabetically. The first accession is not a leading or razor protein, and nothing in this repository names one. ## Datasets - [PXD001054: Redox Proteome of Skeletal Muscle](datasets/PXD001054.html): 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. - [PXD002467: Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats](datasets/PXD002467.html): 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. - [PXD004916: Spermidine treated mouse Heart LC-MS/MS](datasets/PXD004916.html): 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. - [PXD005014: Proteome of Young and Old Murine Diaphragm and Associaated Changes in Contractile Properties](datasets/PXD005014.html): 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. - [PXD005123: Somatic increase of CCT8 mimics proteostasis of human pluripotent stem cells and extends C. elegans lifespan](datasets/PXD005123.html): 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. - [PXD006023: AGK human LC-MSMS project part I (proteome)](datasets/PXD006023.html): 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. - [PXD006216: Chemotherapy-induced cellular senescence is characterized by aberrant lipid regulation and lipid peroxidation](datasets/PXD006216.html): 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. - [PXD006578: Aging-related proteome alterations in B cells may predispose for chronic lymphocytic leukemia - cytoplasmic proteins of CLL cells](datasets/PXD006578.html): 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. - [PXD006589: Aging-related proteome alterations in B cells may predispose for chronic lymphocytic leukemia - nuclear proteins of CLL cells](datasets/PXD006589.html): 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. - [PXD006815: Changes in glycogen metabolism machinery are associated with brain aging. Proteomic and immunofluorescent evidence for a](datasets/PXD006815.html): 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. - [PXD006898: Quantitative proteomics of a human fetal ovary development timecourse](datasets/PXD006898.html): 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. - [PXD007035: Loss-of-function of ubiquitin ligase adaptor LZTR1 triggers human disease by dysregulating RAS ubiquitination](datasets/PXD007035.html): 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. - [PXD007049: Loss-of-function of ubiquitin ligase adaptor LZTR1 triggers human disease by dysregulating RAS ubiquitination](datasets/PXD007049.html): 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. - [PXD007188: Mevalonate pathway activity is a key determinant of radiation sensitivity in head and neck cancer](datasets/PXD007188.html): 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. - [PXD007906: A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cell line](datasets/PXD007906.html): 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. - [PXD007999: NRF2-dependent ECM - Nrf2-Mediated Fibroblast Reprogramming Drives Cellular Senescence by Targeting the Matrisome](datasets/PXD007999.html): 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. - [PXD008050: UVA and to UV-oxidized lipids proteomic regulation of the human keratinocytes](datasets/PXD008050.html): 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. - [PXD008344: Human brain LC-MS/MS - Brain Citrullination Patterns and T Cell Reactivity of Cerebrospinal Fluid-Derived CD4+ T Cells in Multiple Sclerosis](datasets/PXD008344.html): 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. - [PXD008934: Characterization of proteomic changes in human heart failure](datasets/PXD008934.html): 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. - [PXD008990: Glycomic and Proteomic changes in aging brain nigrostriatal pathway](datasets/PXD008990.html): 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. - [PXD009212: Proteome profiling in aging rat brain by LC-MS/MS](datasets/PXD009212.html): 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. - [PXD009430: Modulation of the ATM / autophagy pathway tips the balance between senescence and apoptosis in response to a quadruplex ligand](datasets/PXD009430.html): 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. - [PXD010091: miR-181a Restores Mitochondrial Dynamics in Skeletal Muscle Ageing](datasets/PXD010091.html): 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. - [PXD010115: Quantification of the Soluble Receptor of Advanced Glycation End-Products (sRAGE) by LC-MS Without the Use of Affinity Enrichment](datasets/PXD010115.html): 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. - [PXD010820: O-GlcNAcylation enhances double strand break repair, promotes cancer cell proliferation and prevents therapy-induced senescence in irradiated tumors](datasets/PXD010820.html): 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. - [PXD011314: Profiling of Methylglyoxal Blood Metabolism and Advanced Glycation End-Product Proteome using a Chemical Probe](datasets/PXD011314.html): 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. - [PXD011740: Translational regulation contributes to the secretory response of chondrocytic cells following exposure to Interleukin-1B](datasets/PXD011740.html): 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. - [PXD012213: Effects of Caloric Restriction with Protein Supplementation on Plasma Protein Profiles in Middle-Aged Women with Metabolic Syndrome – A Preliminary Open Study](datasets/PXD012213.html): 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. - [PXD012307: An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics](datasets/PXD012307.html): 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. - [PXD012753: Young, old, OVX mouse Skin LC-MSMS, 3M Urea extraction](datasets/PXD012753.html): 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. - [PXD012754: Ageing Mouse Skin LC-MSMS, NaCl extraction](datasets/PXD012754.html): 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. - [PXD013240: Intracellular proteome (SDS/Na-DoC) extract from EP/LP MSCs grown on soft/stiff hydrogels for 4 days](datasets/PXD013240.html): 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. - [PXD013640: Keap-1-mediated S-nitrosylation of NOX4 hampers oxidative damage in endothelium](datasets/PXD013640.html): 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. - [PXD014097: Auto-phosphorylation at serine 166 regulates RIP kinase 1 mediated cell death and inflammation](datasets/PXD014097.html): 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. - [PXD014098: CLUH-dependent RNA granules coordinate mitochondrial catabolic pathways with mTORC1 signaling and mitophagy](datasets/PXD014098.html): 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. - [PXD014274: Proteomic and unbiased post-translational modification profiling of amyloid plaques and surrounding tissue in a transgenic mouse model of Alzheimer’s disease](datasets/PXD014274.html): 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. - [PXD014416: Spatiotemporal proteomics of hormone treated mice (urine across time, prostate tissue)](datasets/PXD014416.html): 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. - [PXD015079: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix](datasets/PXD015079.html): 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. - [PXD015170: The GID Ubiquitin Ligase Complex is a Regulator of AMPK Activity and Organismal Lifespan](datasets/PXD015170.html): 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. - [PXD015239: Epigenetic contributions to hemisphere asymmetry in healthy brain, aging, and Parkinson’s disease](datasets/PXD015239.html): 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. - [PXD015729: Murine hippocampus after radiation LC-MSMS](datasets/PXD015729.html): 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. - [PXD016430: MiR-29 coordinates age-dependent plasticity brakes in the adult visual cortex](datasets/PXD016430.html): 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. - [PXD016793: Proteomics analysis of rat liver after disulfiram treatment](datasets/PXD016793.html): 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. - [PXD017058: Astrocyte Support for Oligodendrocyte Differentiation can be Conveyed via Extracellular Vesicles but Diminishes with Age](datasets/PXD017058.html): 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. - [PXD017475: The lncRNA MIR31HG regulates the senescence associated secretory phenotype](datasets/PXD017475.html): 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. - [PXD017505: Autofluorescence positive and negative microglia constitute novel subsets found in healthy brain.](datasets/PXD017505.html): 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. - [PXD017944: Proteomic analysis of scleraxis mutant tendon](datasets/PXD017944.html): 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. - [PXD018097: YME1L1 KnockOut MEF Cells Whole Proteomics](datasets/PXD018097.html): 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. - [PXD018315: Identification of proteins that interact with the lncRNA Sarrah](datasets/PXD018315.html): 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. - [PXD018399: Reduced proteasome activity in the aging brainresults in ribosome stoichiometry loss and aggregation](datasets/PXD018399.html): 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. - [PXD018545: Endoplasmic Reticulum Stress-mediated Mitochondrial Dysfunction in Aged Hearts](datasets/PXD018545.html): 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. - [PXD018655: Proteomic analysis of small extracellular vesicles derived from human ESCs](datasets/PXD018655.html): 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. - [PXD018969: Keap1 governs ageing-induced protein aggregation in endothelial cells](datasets/PXD018969.html): 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. - [PXD018999: A dichotomous response to chronic fetal hypoxia preprograms aging already during kidney development](datasets/PXD018999.html): 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. - [PXD019279: Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss](datasets/PXD019279.html): 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. - [PXD019849: Nerv. System Specific Yme1l KO (NYKO) Mice Retina Samples (30-31wks old)](datasets/PXD019849.html): 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. - [PXD020462: Oxidative damage signatures in human bone collagen from Pompeii and Herculaneum.](datasets/PXD020462.html): 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. - [PXD021069: Matrix reverses immortalization-mediated stem cell fate determination](datasets/PXD021069.html): 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. - [PXD021762: Mitochondrial mistranslation is modulated by metabolic stress](datasets/PXD021762.html): 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. - [PXD022128: A genome-wide screen for essentiality upon telomerase inhibition identifies a novel p53 regulator, C16ORF72/TAPR1](datasets/PXD022128.html): 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. - [PXD022180: Mytho, An Uncharacterized Gene that Controls Longevity and WIPI2-dependent Autophagy](datasets/PXD022180.html): 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. - [PXD022196: Chaperone-mediated autophagy sustains hematopoietic stem cell function](datasets/PXD022196.html): 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. - [PXD022227: Col4a5 mouse glomerular extracellular matrix](datasets/PXD022227.html): 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. - [PXD022363: Col4a1 mouse glomerular datasets](datasets/PXD022363.html): 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. - [PXD022393: Circadian Regulation of Protein Cargo in Exosomes](datasets/PXD022393.html): 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. - [PXD022678: The landscape of molecular chaperones across human tissues reveals a layered architecture of core-variable chaperones](datasets/PXD022678.html): 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. - [PXD022737: proteomic changes in aging rats treated with the cognitive enhancer CE-123](datasets/PXD022737.html): 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. - [PXD023381: Transcriptional and proteomic characterization of telomere-induced senescence in a human alveolar epithelial cell line](datasets/PXD023381.html): 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. - [PXD024216: Shotgun-based Proteomics of Extracellular Vesicles in Alzheimer’s Disease Reveals Biomarkers Involved in Immunological and Coagulation Pathways](datasets/PXD024216.html): 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. - [PXD024478: RNA polymerase I transcription disturbances lead to instable ribosomes in Cockayne syndrome](datasets/PXD024478.html): 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. - [PXD024633: Mitochondrial mistranslation modulated by metabolic stress causes cardiovascular disease and reduced life-span](datasets/PXD024633.html): 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. - [PXD024685: Proteomic analyses of non-preconditioned murine kidneys pre- and post-IRI in comparison to kidneys after preconditioning by hypoxia or caloric restriction](datasets/PXD024685.html): 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. - [PXD024803: CHD6 IP from human induced pluripotent stem cells LC-MS-MS](datasets/PXD024803.html): 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. - [PXD025240: Hippocampal disruptions of synaptic and astrocyte metabolism during early amyloid pathology in the 5xFAD mouse model of Alzheimer’s disease](datasets/PXD025240.html): 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. - [PXD025280: Early- and late-passage primary human mesemchymal stem cells subjected to 2 hour heat shock](datasets/PXD025280.html): 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. - [PXD025321: Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia](datasets/PXD025321.html): 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. - [PXD025503: Obesity causes irreversible mitochondria failure in visceral adipose tissue despite successful anti-obesogenic lifestyle](datasets/PXD025503.html): 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. - [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](datasets/PXD026219.html): 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. - [PXD026335: Mouse Heart SS-31 Proteome and Phosphoproteome](datasets/PXD026335.html): 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. - [PXD026608: Integrated analysis of proteomics and phosphoproteomics on rat hearts with aging and hypertension](datasets/PXD026608.html): 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. - [PXD026934: Mitochondria regulate dietary lipid processing in enterocytes](datasets/PXD026934.html): 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. - [PXD027318: Identification of a Proteomic Signature of Senescence in Primary Human Mammary Epithelial Cells](datasets/PXD027318.html): 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. - [PXD027526: Mapping sites of carboxymethyllysine modification on proteins reveals consequences for proteostasis and cell proliferati](datasets/PXD027526.html): 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. - [PXD027734: Proximity-biotinylation (BioID) to dissect cytoplasmic p53 signaling networks under nutrient stress](datasets/PXD027734.html): 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. - [PXD027754: Metabolic reprogramming during hyperammonemia targets mitochondrial function and post-mitotic senescence](datasets/PXD027754.html): 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. - [PXD027971: Simple, single-shot phosphoproteomic analysis of heat-stable tau](datasets/PXD027971.html): 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. - [PXD028157: Proteomics quantification of striatal fraction from DAT-KO and WT rats](datasets/PXD028157.html): 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. - [PXD028590: Amphiregulin mediates non-cell-autonomous effect of senescence on reprogramming](datasets/PXD028590.html): 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. - [PXD028852: Proteins enriched on damaged lysosomes in 293T](datasets/PXD028852.html): 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. - [PXD028865: Unbiased in vivo exploration of nuclear bodies-enhanced sumoylation reveals that PML orchestrates embryonic stem cell fa](datasets/PXD028865.html): 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. - [PXD028975: Engineering Extracellular Vesicles by Three-dimensional Dynamic Culture of Human Mesenchymal Stem Cells](datasets/PXD028975.html): 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. - [PXD029116: Articular cartilage proteome differentiates by zones during osteoarthritis](datasets/PXD029116.html): 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. - [PXD030773: The proto-oncogene TCL1A deregulates mitotic checkpoint transition and genomic stability in CLL](datasets/PXD030773.html): 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. - [PXD030776: The proto-oncogene TCL1A deregulates mitotic checkpoint transition and genomic stability in CLL](datasets/PXD030776.html): 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. - [PXD030939: A compound-based therapy approach for epidermolysis bullosa simplex (EBS)](datasets/PXD030939.html): 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. - [PXD031223: Chronic Aicar Treatment Identifies Sex-specific Phenotypes in the Aging Mouse Heart](datasets/PXD031223.html): 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. - [PXD031604: Analysis of 20-HETE supplementation in calorically restricted C57Bl6 mice](datasets/PXD031604.html): 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. - [PXD032040: Translational specialization in pluripotency by RBPMS poises future lineage-decisions](datasets/PXD032040.html): 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. - [PXD032044: Characterization of the skeletal muscle proteome in under-nourished old rats](datasets/PXD032044.html): 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. - [PXD032046: Translational specialization in pluripotency by RBPMS poises future lineage-decisions](datasets/PXD032046.html): 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. - [PXD032202: Global and comparative proteome signatures in the lens capsule, trabecular meshwork, and iris of patients with pseudoexfoliation glaucoma](datasets/PXD032202.html): 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. - [PXD032240: Unbiased in vivo exploration of nuclear bodies-enhanced sumoylation reveals that PML orchestrates embryonic stem cell fa](datasets/PXD032240.html): 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. - [PXD032757: The role of extracellular vesicles in synovial fibroblast senescence](datasets/PXD032757.html): 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. - [PXD033430: Dysregulated cellular redox status during hyperammonemia causes mitochondrial dysfunction by inhibiting sirtuin mediated](datasets/PXD033430.html): 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. - [PXD034432: Tracking prostate carcinogenesis over time through urine proteome profiling in an animal model: an exploratory approach](datasets/PXD034432.html): 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. - [PXD034465: Surface proteome profiling of p53-restorable murine liver cancer cells](datasets/PXD034465.html): 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. - [PXD034590: Profiling of purified autophagic vesicle content and degradome in the maturing and aging brain](datasets/PXD034590.html): 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. - [PXD035107: Global phosphoproteomic profiling of skeletal muscle in ovarian-hormone deficient mice](datasets/PXD035107.html): 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. - [PXD035149: ORP6 regulates astrocytic cholesterol metabolism and brain Aβ deposition](datasets/PXD035149.html): 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. - [PXD035171: Natural aging and ovariectomy induces parallel phosphoproteomic alterations in skeletal muscle of female mice](datasets/PXD035171.html): 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. - [PXD035299: Nuclear protein expression profiling of IMR90 RAS cells compared to IMR90 Control cells](datasets/PXD035299.html): 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. - [PXD035412: Proteomics analysis of tissue aging nucleic acid binding proteins](datasets/PXD035412.html): 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. - [PXD035446: Extracellular vesicle-derived miRNAs improve stem cell-based therapeutic approaches in muscle wasting conditions.](datasets/PXD035446.html): 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. - [PXD036557: Modelling Premature Cardiac Aging with Induced Pluripotent Stem Cells From a Hutchinson-Gilford Progeria Syndrome Patient](datasets/PXD036557.html): 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. - [PXD037230: Scleraxis-lineage cells are required for tendon homeostasis and their depletion induces an accelerated extracellular mat](datasets/PXD037230.html): 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. - [PXD038328: Organ protection by caloric restriction depends on activation of the de novo NAD+ synthesis pathway](datasets/PXD038328.html): 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. - [PXD038718: An NPAS4:NuA4 complex couples synaptic activity to DNA repair](datasets/PXD038718.html): 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. - [PXD039172: Proteome of the cortex of old Pink1-SNCA A53T double mutant Parkinson mice](datasets/PXD039172.html): 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. - [PXD041139: Proteomic analysis reveals insufficient folliculogenesis in Aging Female associates with infertility](datasets/PXD041139.html): 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. - [PXD041376: Profiling of purified autophagic vesicle content and degradome in the maturing and aging brain - Part II](datasets/PXD041376.html): 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. - [PXD041660: A Defective Extracellular Matrix/Kindlin-2/Actin/ERK Mechanosensing Pathway Affects Fibroblast-To-Myofibroblast Transiti](datasets/PXD041660.html): 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. - [PXD041766: Remodeling of the focal adhesion complex by hydrogen-peroxide- induced senescence](datasets/PXD041766.html): 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. - [PXD042301: Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process.](datasets/PXD042301.html): 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. - [PXD043001: Proteomic characterizationof the circle of Willis during aging](datasets/PXD043001.html): 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. - [PXD043644: Liver-derived plasminogen mediates muscle stem cell expansion during caloric restriction through the plasminogen recepto](datasets/PXD043644.html): 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. - [PXD043779: Evaluation of the secretome of senescent melanoma cells and the impact of silencing Mfn1 on the senescence-associated se](datasets/PXD043779.html): 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. - [PXD043964: Luminal cerebrovascular proteomic changes during aging](datasets/PXD043964.html): 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. - [PXD044227: Food perception liver phosphoproteome induced by caged food and POMC neuron activation](datasets/PXD044227.html): 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. - [PXD044453: Age-Dependent Effects of Voluntary Exercise on Urinary Voiding Function and Frailty-Related Metrics in Mice](datasets/PXD044453.html): 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. - [PXD044773: Cell-specific crosstalk proteomics reveals cathepsin B signaling as a driver of glioblastoma malignancy near the subventricular zone](datasets/PXD044773.html): 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. - [PXD044996: LC-MS/MS analysis of isolated murine brain endothelial cells (BECs) from 3-, 6-, 12-, and 18-months-old mice and Apoe-KO](datasets/PXD044996.html): 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. - [PXD045821: Intracellular Iron Accumulation Facilitates Mycobacterial Infection in Old Mouse Macrophages](datasets/PXD045821.html): 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. - [PXD045861: Myelin-axon interface disruption uncovered by subcellular proteomics and imaging of Alzheimer’s human brain](datasets/PXD045861.html): 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. - [PXD045887: An Intra-Individual Paired Mass Spectrometry dataset for decoding Solar-Induced Proteomic Changes in Facial Skin](datasets/PXD045887.html): 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. - [PXD047288: Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain](datasets/PXD047288.html): 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. - [PXD047289: Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain](datasets/PXD047289.html): 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. - [PXD047292: Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain](datasets/PXD047292.html): 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. - [PXD047293: Protein degradation targets in hippocampus and retrosplenial cortex of the aged brain](datasets/PXD047293.html): 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. - [PXD048393: Acetyl-CoA Carboxylase Obstructs CD8+ T-Cell Lipid Utilization in the Tumor Microenvironment](datasets/PXD048393.html): 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. - [PXD048720: Proteomic analysis of a rat streptozotocin model shows dysregulated biological pathways implicated in Alzheimer’s Disease](datasets/PXD048720.html): 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. - [PXD048877: Egr1 is a master regulator of regenerative senescence and cardiac repair](datasets/PXD048877.html): 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. - [PXD049018: BJ cyto-nuclear translocation upon STING activation](datasets/PXD049018.html): 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. - [PXD049957: Phosphoproteomics of consecuively active AKT in liver and Insulin stimulated primary Hepatocytes](datasets/PXD049957.html): 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. - [PXD050351: Targeting upstream Hippo-pathway kinases releases the scaffolder WWC1 to promote synaptic plasticity and long-term memory in mice](datasets/PXD050351.html): 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. - [PXD051203: Protein degradation targets in the retrosplenial cortex of the female aged brain](datasets/PXD051203.html): 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. - [PXD051644: Protein degradation targets in hippocampus of the aged brain following context exposure](datasets/PXD051644.html): 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. - [PXD051715: Age-related proteostatic imbalance exacerbates heart failure with preserved ejection fraction pathogenesis in old mice](datasets/PXD051715.html): 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. - [PXD052189: Microglial-derived C1q integrates into neuronal ribonucleoprotein complexes and impacts protein homeostasis in the aging](datasets/PXD052189.html): 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. - [PXD052631: G-CSF/NAMPT signaling drives neutrophil dysfunction and enhances bacterial infection susceptibility in cancer patients](datasets/PXD052631.html): 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. - [PXD052797: Increased levels of extracellular matrix proteins in extracellular vesicles from brains of aged mice.](datasets/PXD052797.html): 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. - [PXD053288: RyR2-mediated calcium leak increases glyoxalase I in the aging brain](datasets/PXD053288.html): 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. - [PXD054290: Mouse bone marrow-derived macrophages (BMDMs) loaded with atherogenic LDL](datasets/PXD054290.html): 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. - [PXD055228: GPC3-mediated metabolic rewiring of diabetic mesenchymal stromal cells enhances their cardioprotective functions via pyr](datasets/PXD055228.html): 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. - [PXD056276: SORLA upregulation suppresses global pathological effects in aged tauopathy mouse brain](datasets/PXD056276.html): 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. - [PXD056433: M1 polyubiquitin targets in the hippocampus of young and aged male rats following contextual fear conditioning](datasets/PXD056433.html): 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. - [PXD056458: M1 polyubiquitin targets in the hippocampus across the lifespan](datasets/PXD056458.html): 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. - [PXD057407: Proteomic and Phosphoproteomic Signatures of Aging Mouse Liver](datasets/PXD057407.html): 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. - [PXD057409: Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease_C2C12 myotube p](datasets/PXD057409.html): 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. - [PXD057490: Synaptic phosphoproteome modifications and cortical circuit dysfunction are linked to the early-stage progression of alpha-synuclein pathology](datasets/PXD057490.html): 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. - [PXD057499: Synaptic phosphoproteome modifications and cortical circuit dysfunction are linked to the early-stage progression of alpha-synuclein pathology](datasets/PXD057499.html): 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. - [PXD057502: Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease-C2C12 myotube p](datasets/PXD057502.html): 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. - [PXD057544: Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease- C2C12 myotube ](datasets/PXD057544.html): 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. - [PXD057545: Chaperone-mediated autophagy sex-specifically regulates neuronal activity by remodeling the synaptic proteome](datasets/PXD057545.html): 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. - [PXD057554: Integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease-Mouse skeletal ](datasets/PXD057554.html): 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. - [PXD058082: Major toxin composition of particulate matter from a coal-fired power plant and its proteomics-associated toxicological ](datasets/PXD058082.html): 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. - [PXD058156: Temozolomide Induces Glioblastoma Dedifferentiation into Highly Malignant Stem-like Cells Through Senescence-Associated Reprogramming via HIF1α/HIF2α Regulation](datasets/PXD058156.html): 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. - [PXD058248: K63 polyubiquitin targets in the hippocampus across the lifespan](datasets/PXD058248.html): 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. - [PXD058253: K63 polyubiquitin targets in the amygdala across the lifespan](datasets/PXD058253.html): 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. - [PXD058611: Enhanced non-enzymatic H2S generation extends lifespan and healthspan in male mice](datasets/PXD058611.html): 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. - [PXD058775: DNA Damage in Macrophages Drives Immune Autoreactivity via Nuclear Antigen Presentation](datasets/PXD058775.html): 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. - [PXD058855: KAT5-mediated acetylation of PC4 facilitates DNA repair by promoting chromatin reorganization](datasets/PXD058855.html): 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. - [PXD058971: Multi-omics Analysis Shed Light on the Extracellular Role of PCMT1](datasets/PXD058971.html): 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. - [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](datasets/PXD059520.html): 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. - [PXD059818: Simultaneous profiling of native-state proteomes and transcriptomes of brain cell types using proximity labeling](datasets/PXD059818.html): 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. - [PXD060832: Mitochondrial regulator PGC-1a in neuronal metabolism and brain aging](datasets/PXD060832.html): 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. - [PXD060982: mTOR orchestrates sequential phases of ependymal cell differentiation by acting on their alternative cell cycle and cent](datasets/PXD060982.html): 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. - [PXD061069: The SET1/COMPASS subunit RBBP5 orchestrates epigenetic control of global proteostasis and the 12h oscillator to safeguar](datasets/PXD061069.html): 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. - [PXD061654: The mammalian longevity associated acetylome](datasets/PXD061654.html): 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. - [PXD064236: DLX2-FLAG IP-MS in embryonic bodies (EBs): Protein complexes identification](datasets/PXD064236.html): 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. - [PXD067102: Young and aged T cells LC-MS/MS](datasets/PXD067102.html): 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. - [PXD067622: DNA-Protein Crosslinks Promote cGAS-STING-driven Premature Aging and Embryonic Lethality](datasets/PXD067622.html): 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. - [PXD068498: Reduced IGF-1 signaling fails to limit Alzheimer’s disease progression in a novel rat model of IGF-1R haploinsufficiency](datasets/PXD068498.html): 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. - [PXD069093: Kinome profiling of osteosarcoma patient-derived xenograft TT2 treated with palbociclib](datasets/PXD069093.html): 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. - [PXD071171: Mitochondrial IntegrityMitochondrial Integrity Modulates mTOR Signaling and Podocyte Function Modulates mTOR Signaling and Podocyte Function](datasets/PXD071171.html): 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. - [PXD073846: mtDNA alterations determine myoblast differentiation and disrupt skeletal muscle architecture](datasets/PXD073846.html): 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. - [PXD073999: Mechanisms of the antiproliferative effects of SIRT6 inhibition in melanoma: A multi-omics analysis](datasets/PXD073999.html): 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. - [PXD075372: Senescence inhibition by rapamycin mitigates radiation-induced atherosclerosis characteristics in human coronary endothelial cells](datasets/PXD075372.html): 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. - [PXD077298: Sinapic acid promotes disaggregation and extracellular secretion of polyglutamine repeats containing aggregates and resc](datasets/PXD077298.html): 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. - [PXD082596: Proteomic comparison of tail tendons from Col1a2 mutant mice](datasets/PXD082596.html): 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. ## Access - [datasets.json](datasets.json): a small index, one entry per dataset, each naming its full JSON (`datasets/.json`: every fact on its page, all findings and modifications). - [proteins/index.json](proteins/index.json): which datasets have accepted evidence for a protein. It lists every protein shard by accession prefix: fetch the shard whose prefix is the longest one the accession starts with. A gene symbol is in `genes/.json`, which gives its accessions. - [MCP server](https://github.com/smith-chem-wisc/dataRepo/blob/master/docs/mcp.md): `datarepo mcp --catalog ` serves a catalog to an agent over stdio (describe, search, read-only SQL). - [Schema](https://github.com/smith-chem-wisc/dataRepo/tree/master/docs/schema): every table and column, with its meaning. - Bulk Parquet download: not published yet. ## Optional - [Source code](https://github.com/smith-chem-wisc/dataRepo): the ingester and catalog builder that made this data. - [Limitations](https://github.com/smith-chem-wisc/dataRepo/blob/master/docs/limitations.md): what the repository does not yet hold.