Generated summary
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.
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, 4 warnings and 1 for information
count_mismatch warning
The bundle holds 55829 where the producer reported 55832 (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 55829 where the producer reported 55832 (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 25042 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1327 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 25042 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1327 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: 716 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: 716 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
52 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
52 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 | 55,829 |
| Peptidoforms at 1% FDR | 8,164 |
| Protein groups at 1% FDR | 912 |
| PTM sites | 4,450 |
| Quantitative values | 68,137 |
| PSMs, all (including decoys and sub-threshold) | 127,043 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 35.0% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.4% |
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
- 9 / 9
- 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 | 684 |
| Deamidation on Q | UNIMOD:7 | 422 |
| NEM:2H(5) on C | UNIMOD:776 | 369 |
| Deamidation on N | UNIMOD:7 | 277 |
| Oxidation on M | UNIMOD:35 | 274 |
| Sodium on E | UNIMOD:30 | 271 |
| Sodium on D | UNIMOD:30 | 200 |
| Calcium on E | UNIMOD:951 | 197 |
| Calcium on D | UNIMOD:951 | 162 |
| Magnesium on E | UNIMOD:956 | 122 |
| Nethylmaleimide+water on C | — | 122 |
| Magnesium on D | UNIMOD:956 | 117 |
| Ammonia loss on N | UNIMOD:385 | 85 |
| N-acetylalanine on A | UNIMOD:1 | 74 |
| Hydroxylation on P | UNIMOD:35 | 60 |
| Acetylation on X | UNIMOD:1 | 49 |
| Phosphorylation on S | UNIMOD:21 | 48 |
| Citrullination on R | UNIMOD:7 | 41 |
| Hydroxylation on K | UNIMOD:35 | 35 |
| Crotonylation on K | UNIMOD:1363 | 34 |
| Phosphoserine on S | UNIMOD:21 | 30 |
| N-acetylmethionine on M | UNIMOD:1 | 28 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 25 |
| Hydroxylation on N | UNIMOD:35 | 25 |
| Glutarylation on K | UNIMOD:1848 | 23 |
| N-acetylserine on S | UNIMOD:1 | 23 |
| Water Loss on E | UNIMOD:27 | 23 |
| Phosphorylation on T | UNIMOD:21 | 21 |
| Methylation on K | UNIMOD:34 | 20 |
| N6-acetyllysine on K | UNIMOD:1 | 19 |
| Potassium on D | UNIMOD:530 | 19 |
| Potassium on E | UNIMOD:530 | 19 |
| Hydroxybutyrylation on K | — | 18 |
| Trimethylation on K | UNIMOD:37 | 18 |
| Fe[II] on D | UNIMOD:952 | 17 |
| Dimethylation on K | UNIMOD:36 | 16 |
| Butyrylation on K | UNIMOD:1289 | 15 |
| Formylation on K | UNIMOD:122 | 14 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 14 |
| Succinylation on K | UNIMOD:64 | 13 |
| 4-hydroxyproline on P | UNIMOD:35 | 12 |
| Fe[II] on E | UNIMOD:952 | 11 |
| HexNAc on T | UNIMOD:43 | 11 |
| Dimethylation on R | UNIMOD:36 | 10 |
| HexNAc on S | UNIMOD:43 | 10 |
| N-acetylthreonine on T | UNIMOD:1 | 10 |
| Phosphothreonine on T | UNIMOD:21 | 10 |
| Acetylation on K | UNIMOD:1 | 9 |
| Carbamyl on X | UNIMOD:5 | 9 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 8 |
| Malonylation on K | UNIMOD:747 | 7 |
| N6-succinyllysine on K | — | 7 |
| Carbamyl on K | UNIMOD:5 | 6 |
| Methylation on R | UNIMOD:34 | 6 |
| Sulfonation on Y | UNIMOD:40 | 6 |
| Tele-methylhistidine on H | UNIMOD:34 | 6 |
| Carbamyl on C | UNIMOD:5 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| Phosphorylation on Y | UNIMOD:21 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 4 |
| Pyridoxal phosphate on K | UNIMOD:46 | 4 |
| Carbamyl on M | UNIMOD:5 | 3 |
| Carboxylation on D | UNIMOD:299 | 3 |
| Carboxylation on E | UNIMOD:299 | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| ADP-ribosylation on S | UNIMOD:213 | 2 |
| Carboxylation on K | UNIMOD:299 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Ammonia loss on C | UNIMOD:385 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Glu to PyroGlu on Q | UNIMOD:28 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| Omega-N-methylarginine on R | 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
836a36ff2e21d338, written 2026-10-29T09:47:25+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