Generated summary
PXD057544 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and enrichment: acetyl. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 26,740 PSMs, 2,794 peptidoforms and 1,223 protein groups, and the repository holds 2,489 PTM sites for it. 5 open warnings about it are recorded.
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 1 for information
low_core_use warning
7.56 avg cores of 32 allowed (S5)
7.56 avg cores of 32 allowed (S5)
low_id_rate warning
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 26740/223365 = 11.97% of MS2 identified (S3)
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 26740/223365 = 11.97% of MS2 identified (S3)
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 5436 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 418 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 5436 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 418 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: 109 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: 109 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.
occupancy_decoy_groups info
6 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
6 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 | 26,740 |
| Peptidoforms at 1% FDR | 2,794 |
| Protein groups at 1% FDR | 1,223 |
| PTM sites | 2,489 |
| Quantitative values | 49,665 |
| PSMs, all (including decoys and sub-threshold) | 474,854 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 12.0% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.7% |
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
- acetyl
- Instrument vendor
- not recorded
- Runs / samples
- 9 / 9
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- b8b36ebf6016
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 1,005 |
| Carbamidomethyl on C | UNIMOD:4 | 925 |
| N6-acetyllysine on K | UNIMOD:1 | 379 |
| Hydroxylation on P | UNIMOD:35 | 27 |
| Phosphoserine on S | UNIMOD:21 | 24 |
| N-acetylalanine on A | UNIMOD:1 | 21 |
| N-acetylserine on S | UNIMOD:1 | 14 |
| Acetylation on K | UNIMOD:1 | 10 |
| Phosphothreonine on T | UNIMOD:21 | 8 |
| HexNAc on T | UNIMOD:43 | 7 |
| Hydroxylation on K | UNIMOD:35 | 6 |
| HexNAc on S | UNIMOD:43 | 5 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 4 |
| Acetylation on X | UNIMOD:1 | 3 |
| N6-butyryllysine on K | UNIMOD:1289 | 3 |
| N6-methyllysine on K | UNIMOD:34 | 3 |
| Omega-N-methylarginine on R | UNIMOD:34 | 3 |
| 4-hydroxyproline on P | UNIMOD:35 | 2 |
| Methylation on K | UNIMOD:34 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 1 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylthreonine on T | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 1 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| Phosphorylation on S | UNIMOD:21 | 1 |
| Phosphorylation on T | UNIMOD:21 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| Trimethylation on K | UNIMOD:37 | 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
00b7d9c490b115d5, written 2026-10-29T10:07:50+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