Generated summary
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.
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
count_mismatch warning
The bundle holds 12200 where the producer reported 12199 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 12200 where the producer reported 12199 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
count_mismatch warning
The bundle holds 217078 where the producer reported 217145 (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 217078 where the producer reported 217145 (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.
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 83402 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3849 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 83402 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3849 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: 990 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: 990 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
234 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
234 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 | 217,078 |
| Peptidoforms at 1% FDR | 12,200 |
| Protein groups at 1% FDR | 1,402 |
| PTM sites | 6,526 |
| Quantitative values | 288,663 |
| PSMs, all (including decoys and sub-threshold) | 410,443 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 18.1% |
| 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
- none
- Instrument vendor
- not recorded
- Runs / samples
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 089bcc7b11dc
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Nethylmaleimide on C | UNIMOD:108 | 1,694 |
| Oxidation on M | UNIMOD:35 | 647 |
| Deamidation on N | UNIMOD:7 | 565 |
| Deamidation on Q | UNIMOD:7 | 517 |
| NEM:2H(5) on C | UNIMOD:776 | 491 |
| Sodium on D | UNIMOD:30 | 169 |
| Sodium on E | UNIMOD:30 | 166 |
| Ammonia loss on N | UNIMOD:385 | 148 |
| Nethylmaleimide+water on C | — | 130 |
| Hydroxylation on P | UNIMOD:35 | 110 |
| Magnesium on D | UNIMOD:956 | 106 |
| N-acetylalanine on A | UNIMOD:1 | 100 |
| Magnesium on E | UNIMOD:956 | 88 |
| Calcium on D | UNIMOD:951 | 81 |
| Calcium on E | UNIMOD:951 | 76 |
| Acetylation on X | UNIMOD:1 | 62 |
| Citrullination on R | UNIMOD:7 | 62 |
| Hydroxylation on N | UNIMOD:35 | 62 |
| Hydroxylation on K | UNIMOD:35 | 56 |
| Carbamyl on X | UNIMOD:5 | 44 |
| Phosphorylation on S | UNIMOD:21 | 44 |
| Phosphoserine on S | UNIMOD:21 | 43 |
| Methylation on K | UNIMOD:34 | 35 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 34 |
| Glutarylation on K | UNIMOD:1848 | 34 |
| Potassium on D | UNIMOD:530 | 34 |
| N-acetylmethionine on M | UNIMOD:1 | 33 |
| N-acetylserine on S | UNIMOD:1 | 29 |
| Cu[I] on E | UNIMOD:531 | 28 |
| Dimethylation on K | UNIMOD:36 | 26 |
| Phosphorylation on T | UNIMOD:21 | 25 |
| Hydroxybutyrylation on K | — | 23 |
| Water Loss on E | UNIMOD:27 | 22 |
| Cu[I] on D | UNIMOD:531 | 21 |
| Succinylation on K | UNIMOD:64 | 20 |
| Acetylation on K | UNIMOD:1 | 19 |
| Crotonylation on K | UNIMOD:1363 | 19 |
| Fe[III] on E | UNIMOD:1870 | 19 |
| Potassium on E | UNIMOD:530 | 18 |
| Fe[III] on D | UNIMOD:1870 | 16 |
| Formylation on K | UNIMOD:122 | 16 |
| Trimethylation on K | UNIMOD:37 | 16 |
| Phosphothreonine on T | UNIMOD:21 | 14 |
| Butyrylation on K | UNIMOD:1289 | 13 |
| N6-succinyllysine on K | — | 13 |
| Zinc on E | UNIMOD:954 | 12 |
| N6-acetyllysine on K | UNIMOD:1 | 11 |
| Sulfonation on Y | UNIMOD:40 | 11 |
| HexNAc on S | UNIMOD:43 | 10 |
| Zinc on D | UNIMOD:954 | 10 |
| Methylation on R | UNIMOD:34 | 9 |
| Carbamyl on K | UNIMOD:5 | 8 |
| Fe[II] on E | UNIMOD:952 | 7 |
| HexNAc on T | UNIMOD:43 | 7 |
| N-acetylthreonine on T | UNIMOD:1 | 7 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 7 |
| Fe[II] on D | UNIMOD:952 | 6 |
| Malonylation on K | UNIMOD:747 | 6 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 6 |
| Carboxylation on E | UNIMOD:299 | 5 |
| Nitrosylation on Y | UNIMOD:354 | 5 |
| Carbamyl on C | UNIMOD:5 | 4 |
| Carboxylation on D | UNIMOD:299 | 4 |
| Carboxylation on K | UNIMOD:299 | 4 |
| Glu to PyroGlu on Q | UNIMOD:28 | 4 |
| Nitrosylation on C | UNIMOD:275 | 4 |
| Phosphorylation on Y | UNIMOD:21 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carbamyl on M | UNIMOD:5 | 2 |
| Carbamyl on R | UNIMOD:5 | 2 |
| Dimethylation on R | UNIMOD:36 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-myristoyl glycine on G | UNIMOD:45 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| Ammonia loss on C | UNIMOD:385 | 1 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-methacryllysine on K | — | 1 |
| Omega-N-methylarginine on R | UNIMOD:34 | 1 |
| Pyridoxal phosphate on K | UNIMOD:46 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 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
416b68e7c2f68c93, written 2026-10-29T09:12:47+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct, peptidoforms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group