Generated summary
PXD004916 is a DDA label-free dataset (Mus musculus) with 54 runs, 54 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 227,597 PSMs, 16,301 peptidoforms and 2,001 protein groups, and the repository holds 5,536 PTM sites for it. 8 open warnings about it are recorded.
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, 8 warnings and 1 for information
contaminant_label_unresolved warning
9 protein(s) share a PSM row with proteins of another kind, and the searched databases could not say which they are (not on disk, or in both a target and the contaminant database under TCAmbiguity unknown). Each was given its row's label, contaminant over target, so `is_contaminant` may over-state for them: P08730, P19001, Q6IFZ6, Q6IME9, Q6NXH9.
9 protein(s) share a PSM row with proteins of another kind, and the searched databases could not say which they are (not on disk, or in both a target and the contaminant database under TCAmbiguity unknown). Each was given its row's label, contaminant over target, so `is_contaminant` may over-state for them: P08730, P19001, Q6IFZ6, Q6IME9, Q6NXH9.
cysteine_poor warning
1.23% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
1.23% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
high_contamination warning
13.41% of protein intensity in the worst file, 0.34% median across 54 files (DEF-QC-9 v3.5)
13.41% of protein intensity in the worst file, 0.34% median across 54 files (DEF-QC-9 v3.5)
low_core_use warning
9.63 avg cores of 32 allowed (S5)
9.63 avg cores of 32 allowed (S5)
occupancy_not_stored warning
Of 5727 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1806 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 5727 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1806 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).
sdrf_uncoded warning
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: heart. Match on it as text; it has not been mapped to a term.
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: heart. Match on it as text; it has not been mapped to a term.
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: 74 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: 74 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.
upstream_provenance_changed warning
The search recorded its upstream 'fetch' provenance (run_2026-09-21/PXD004916/02_fetch/provenance.json) with sha256 eb19d153e76e324836ca6229b545560d903b8089c739a7f740588ae4bc51e135, and the file there now has a36406de2c81fe2283ea02dc5f823ebe72566f84fbbf2608a622a983b07ee88b: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the fetch stage is gone unless the producer archived it.
The search recorded its upstream 'fetch' provenance (run_2026-09-21/PXD004916/02_fetch/provenance.json) with sha256 eb19d153e76e324836ca6229b545560d903b8089c739a7f740588ae4bc51e135, and the file there now has a36406de2c81fe2283ea02dc5f823ebe72566f84fbbf2608a622a983b07ee88b: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the fetch stage is gone unless the producer archived it.
occupancy_decoy_groups info
107 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
107 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 | 227,597 |
| Peptidoforms at 1% FDR | 16,301 |
| Protein groups at 1% FDR | 2,001 |
| PTM sites | 5,536 |
| Quantitative values | 364,317 |
| PSMs, all (including decoys and sub-threshold) | 1,658,232 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 30.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.9% |
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
- Thermo
- Runs / samples
- 54 / 54
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 2eb9a52d7f0c
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 4,117 |
| Carbamidomethyl on C | UNIMOD:4 | 588 |
| Hydroxylation on P | UNIMOD:35 | 131 |
| Phosphoserine on S | UNIMOD:21 | 92 |
| N-acetylalanine on A | UNIMOD:1 | 89 |
| N6-acetyllysine on K | UNIMOD:1 | 80 |
| Acetylation on X | UNIMOD:1 | 42 |
| Hydroxylation on K | UNIMOD:35 | 37 |
| N-acetylmethionine on M | UNIMOD:1 | 36 |
| Acetylation on K | UNIMOD:1 | 25 |
| N-acetylserine on S | UNIMOD:1 | 25 |
| N6-succinyllysine on K | — | 24 |
| Methylation on K | UNIMOD:34 | 22 |
| 4-hydroxyproline on P | UNIMOD:35 | 18 |
| Phosphothreonine on T | UNIMOD:21 | 17 |
| Omega-N-methylarginine on R | UNIMOD:34 | 14 |
| Methylation on R | UNIMOD:34 | 11 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 11 |
| HexNAc on T | UNIMOD:43 | 10 |
| N-acetylthreonine on T | UNIMOD:1 | 10 |
| Dimethylation on K | UNIMOD:36 | 9 |
| N-myristoyl glycine on G | UNIMOD:45 | 9 |
| HexNAc on S | UNIMOD:43 | 6 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 5 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 5 |
| Succinylation on K | UNIMOD:64 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Dimethylation on R | UNIMOD:36 | 3 |
| Glutarylation on K | UNIMOD:1848 | 3 |
| Hydroxyproline on P | UNIMOD:35 | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 3 |
| Phosphotyrosine on Y | UNIMOD:21 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-crotonyllysine on K | — | 2 |
| N6-malonyllysine on K | — | 2 |
| Phosphorylation on S | UNIMOD:21 | 2 |
| Phosphorylation on Y | UNIMOD:21 | 2 |
| Trimethylation on K | UNIMOD:37 | 2 |
| (3S)-3-hydroxylysine on K | — | 1 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Malonylation on K | UNIMOD:747 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-glutaryllysine on K | — | 1 |
| N6-methyllysine on K | UNIMOD:34 | 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
d02c7622570083f3, written 2026-10-29T11:35:48+00:00 by ingester 1.4.0- Reconciliation
- every check agreed with the producer's own counts
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group