Generated summary
PXD082596 is a DDA label-free dataset (Mus musculus) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 472,890 PSMs, 23,266 peptidoforms and 3,375 protein groups, and the repository holds 11,841 PTM sites for it. 5 open warnings about it are recorded.
Written from catalog fields only (D17), with no model involved. It says nothing the tables below do not.
Written from catalog fields only (D17), with no model involved. It says nothing the tables below do not.
Open findings
Recorded against this dataset: 0 errors, 5 warnings and 2 for information
count_mismatch warning
The bundle holds 472890 where the producer reported 472897 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 472890 where the producer reported 472897 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
high_contamination warning
16.29% of protein intensity in the worst file, 2.89% median across 24 files (DEF-QC-9 v3.5)
16.29% of protein intensity in the worst file, 2.89% median across 24 files (DEF-QC-9 v3.5)
no_sdrf warning
No SDRF was found for this dataset, so each run was given a synthetic sample of its own. There is no sample metadata: treat every sample as unannotated.
No SDRF was found for this dataset, so each run was given a synthetic sample of its own. There is no sample metadata: treat every sample as unannotated.
occupancy_not_stored warning
Of 42709 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1 segment's accession not determinable from the sequences; 2251 site not in ptm_sites. 'site not in ptm_sites' means the entry's site has no ptm_sites row to key on; 'not determinable' means a cell's segments could not be assigned to its accessions from the sequences (QuantProject DEF-OCC-ACCESSION), which is never guessed. Absence of a row for these sites is therefore not NA. A 'duplicate' is a second entry for a (site, run) that already has a row: one with identical values loses nothing; one with DIFFERENT values means MetaMorpheus wrote two answers and the first in file order was stored (examples in bundle.json occupancy.differing_duplicates; which one should be stored is QuantProject's to define).
Of 42709 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1 segment's accession not determinable from the sequences; 2251 site not in ptm_sites. 'site not in ptm_sites' means the entry's site has no ptm_sites row to key on; 'not determinable' means a cell's segments could not be assigned to its accessions from the sequences (QuantProject DEF-OCC-ACCESSION), which is never guessed. Absence of a row for these sites is therefore not NA. A 'duplicate' is a second entry for a (site, run) that already has a row: one with identical values loses nothing; one with DIFFERENT values means MetaMorpheus wrote two answers and the first in file order was stored (examples in bundle.json occupancy.differing_duplicates; which one should be stored is QuantProject's to define).
unplaced_ptm_sites warning
Some modifications on peptides shared between proteins were not written to ptm_sites for one or more of those proteins, because the peptide could not be located in that protein's sequence and the producer's residue spans cannot be paired with its accessions. Of the (PSM, protein) pairs affected: 1198 named a protein that does not contain the stored peptide -- typically a PSM ambiguous between peptide sequences (level 4 or 5), where this protein carries a different candidate than the first, which is the one stored. Sites on the other proteins of the same PSMs are written. Counts are in bundle.json under protein_databases.
Some modifications on peptides shared between proteins were not written to ptm_sites for one or more of those proteins, because the peptide could not be located in that protein's sequence and the producer's residue spans cannot be paired with its accessions. Of the (PSM, protein) pairs affected: 1198 named a protein that does not contain the stored peptide -- typically a PSM ambiguous between peptide sequences (level 4 or 5), where this protein carries a different candidate than the first, which is the one stored. Sites on the other proteins of the same PSMs are written. Counts are in bundle.json under protein_databases.
collapsed_duplicate_rows info
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 1 identifier(s), 1 row(s) dropped, e.g. PXD082596:A0A6B9UF22;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE92;A0A9L6KEA6 written 2 times; quant_values: 24 identifier(s), 24 row(s) dropped, e.g. PXD082596:20240927_ChangJ_KnoxJ_03:label_free:protein_group:PXD082596:A0A6B9UF22;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE92;A0A9L6KEA6:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 1 identifier(s), 1 row(s) dropped, e.g. PXD082596:A0A6B9UF22;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE92;A0A9L6KEA6 written 2 times; quant_values: 24 identifier(s), 24 row(s) dropped, e.g. PXD082596:20240927_ChangJ_KnoxJ_03:label_free:protein_group:PXD082596:A0A6B9UF22;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE92;A0A9L6KEA6:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
97 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
97 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
What was found
| PSMs at 1% FDR | 472,890 |
| Peptidoforms at 1% FDR | 23,266 |
| Protein groups at 1% FDR | 3,375 |
| PTM sites | 11,841 |
| Quantitative values | 403,511 |
| PSMs, all (including decoys and sub-threshold) | 1,071,814 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 28.7% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 2.3% |
How it was measured
- Organism searched
- Mus musculus (the protein database's organism, not a statement about the samples)
- Acquisition
- DDA
- Quantification
- label_free
- Labelling
- none
- Enrichment
- none
- Instrument vendor
- not recorded
- Runs / samples
- 24 / 24
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 766ecc4f6ae7
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 4,054 |
| Oxidation on M | UNIMOD:35 | 2,514 |
| Deamidation on N | UNIMOD:7 | 843 |
| Hydroxylation on P | UNIMOD:35 | 829 |
| Deamidation on Q | UNIMOD:7 | 381 |
| Hydroxylation on N | UNIMOD:35 | 176 |
| Ammonia loss on N | UNIMOD:385 | 160 |
| Citrullination on R | UNIMOD:7 | 149 |
| Fe[III] on E | UNIMOD:1870 | 145 |
| 4-hydroxyproline on P | UNIMOD:35 | 125 |
| Fe[III] on D | UNIMOD:1870 | 115 |
| Phosphoserine on S | UNIMOD:21 | 115 |
| Sodium on E | UNIMOD:30 | 106 |
| Hydroxylation on K | UNIMOD:35 | 103 |
| N-acetylalanine on A | UNIMOD:1 | 85 |
| Ammonia loss on C | UNIMOD:385 | 78 |
| Phosphorylation on S | UNIMOD:21 | 78 |
| Sodium on D | UNIMOD:30 | 66 |
| Water Loss on E | UNIMOD:27 | 65 |
| Magnesium on E | UNIMOD:956 | 54 |
| Formylation on K | UNIMOD:122 | 53 |
| Phosphorylation on T | UNIMOD:21 | 48 |
| Calcium on E | UNIMOD:951 | 46 |
| Fe[II] on E | UNIMOD:952 | 41 |
| Calcium on D | UNIMOD:951 | 40 |
| Acetylation on X | UNIMOD:1 | 37 |
| Carboxylation on E | UNIMOD:299 | 37 |
| N-acetylmethionine on M | UNIMOD:1 | 37 |
| N-acetylserine on S | UNIMOD:1 | 36 |
| N6-acetyllysine on K | UNIMOD:1 | 30 |
| Methylation on K | UNIMOD:34 | 29 |
| Carbamyl on X | UNIMOD:5 | 28 |
| Carboxylation on D | UNIMOD:299 | 27 |
| Carboxylation on K | UNIMOD:299 | 27 |
| HexNAc on S | UNIMOD:43 | 27 |
| Methylation on R | UNIMOD:34 | 27 |
| HexNAc on T | UNIMOD:43 | 25 |
| Potassium on E | UNIMOD:530 | 24 |
| Magnesium on D | UNIMOD:956 | 23 |
| Fe[II] on D | UNIMOD:952 | 20 |
| Potassium on D | UNIMOD:530 | 17 |
| Cu[I] on E | UNIMOD:531 | 15 |
| Carbamyl on K | UNIMOD:5 | 13 |
| Dimethylation on R | UNIMOD:36 | 13 |
| Omega-N-methylarginine on R | UNIMOD:34 | 13 |
| Zinc on E | UNIMOD:954 | 13 |
| N-acetylthreonine on T | UNIMOD:1 | 11 |
| Acetylation on K | UNIMOD:1 | 10 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 10 |
| Phosphothreonine on T | UNIMOD:21 | 10 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 9 |
| HexNAc on Nxt | UNIMOD:43 | 9 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 9 |
| Butyrylation on K | UNIMOD:1289 | 8 |
| Glu to PyroGlu on Q | UNIMOD:28 | 8 |
| Phosphorylation on Y | UNIMOD:21 | 8 |
| 5-hydroxylysine on K | UNIMOD:35 | 7 |
| Crotonylation on K | UNIMOD:1363 | 7 |
| HexNAc on Nxs | UNIMOD:43 | 7 |
| N6-methyllysine on K | UNIMOD:34 | 7 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 6 |
| Cu[I] on D | UNIMOD:531 | 6 |
| Dimethylation on K | UNIMOD:36 | 6 |
| Sulfonation on Y | UNIMOD:40 | 6 |
| Trimethylation on K | UNIMOD:37 | 5 |
| 3-hydroxyproline on P | UNIMOD:35 | 4 |
| Glutarylation on K | UNIMOD:1848 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| Pros-methylhistidine on H | UNIMOD:34 | 4 |
| Zinc on D | UNIMOD:954 | 4 |
| Carbamyl on R | UNIMOD:5 | 3 |
| Deamidated asparagine on N | UNIMOD:7 | 3 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 3 |
| Nitrosylation on Y | UNIMOD:354 | 3 |
| Tele-methylhistidine on H | UNIMOD:34 | 3 |
| 4-carboxyglutamate on E | UNIMOD:299 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carbamyl on M | UNIMOD:5 | 2 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3'-bromotyrosine on Y | UNIMOD:340 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Allysine on K | UNIMOD:352 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| N6-succinyllysine on K | — | 1 |
Every modification with a site on a target protein, most frequent first. A dash in the UNIMOD
column means the modification has no UNIMOD term in the registry that searched it, not that it is
unknown. One chemistry can appear under two names (UniProt's and MetaMorpheus's); the catalog's
ptm_sites_by_chemistry view merges them.
Data
The Parquet files for this dataset are not published yet.
- Bundle
cb4333005a202eb2, written 2026-10-29T10:24:14+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group