Generated summary
PXD052797 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 416,306 PSMs, 8,103 peptidoforms and 1,591 protein groups, and the repository holds 9,068 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 416306 where the producer reported 416308 (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 416306 where the producer reported 416308 (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
49.22% of protein intensity in the worst file, 4.63% median across 54 files (DEF-QC-9 v3.5)
49.22% of protein intensity in the worst file, 4.63% median across 54 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 37622 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4916 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 37622 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4916 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: 1624 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: 1624 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), 2 row(s) dropped, e.g. PXD052797:O35381;Q64G17;Q9EST5 written 3 times; quant_values: 54 identifier(s), 108 row(s) dropped, e.g. PXD052797:jm_QEHFx_08192022_Arrant_MsBraExo_Mf205_1:label_free:protein_group:PXD052797:O35381;Q64G17;Q9EST5:QuantProject:DEF-PROT-SPC written 3 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), 2 row(s) dropped, e.g. PXD052797:O35381;Q64G17;Q9EST5 written 3 times; quant_values: 54 identifier(s), 108 row(s) dropped, e.g. PXD052797:jm_QEHFx_08192022_Arrant_MsBraExo_Mf205_1:label_free:protein_group:PXD052797:O35381;Q64G17;Q9EST5:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
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 | 416,306 |
| Peptidoforms at 1% FDR | 8,103 |
| Protein groups at 1% FDR | 1,591 |
| PTM sites | 9,068 |
| Quantitative values | 412,262 |
| PSMs, all (including decoys and sub-threshold) | 1,650,804 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 25.3% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 3.5% |
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
- 54 / 54
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 2,953 |
| Carbamidomethyl on C | UNIMOD:4 | 1,923 |
| Deamidation on N | UNIMOD:7 | 676 |
| Deamidation on Q | UNIMOD:7 | 516 |
| Hydroxylation on P | UNIMOD:35 | 500 |
| Hydroxylation on N | UNIMOD:35 | 257 |
| Citrullination on R | UNIMOD:7 | 195 |
| Ammonia loss on N | UNIMOD:385 | 169 |
| Acetylation on K | UNIMOD:1 | 155 |
| Hydroxylation on K | UNIMOD:35 | 129 |
| Carbamyl on X | UNIMOD:5 | 114 |
| Methylation on K | UNIMOD:34 | 97 |
| N-acetylalanine on A | UNIMOD:1 | 91 |
| Acetylation on X | UNIMOD:1 | 67 |
| Sodium on D | UNIMOD:30 | 57 |
| Methylation on R | UNIMOD:34 | 53 |
| Phosphoserine on S | UNIMOD:21 | 53 |
| Sodium on E | UNIMOD:30 | 53 |
| Carbamyl on M | UNIMOD:5 | 51 |
| Phosphorylation on S | UNIMOD:21 | 45 |
| Ammonia loss on C | UNIMOD:385 | 44 |
| Magnesium on D | UNIMOD:956 | 43 |
| N-acetylserine on S | UNIMOD:1 | 34 |
| N-acetylmethionine on M | UNIMOD:1 | 33 |
| Water Loss on E | UNIMOD:27 | 31 |
| Phosphorylation on T | UNIMOD:21 | 27 |
| Magnesium on E | UNIMOD:956 | 24 |
| HexNAc on S | UNIMOD:43 | 23 |
| N6-acetyllysine on K | UNIMOD:1 | 23 |
| Fe[III] on E | UNIMOD:1870 | 21 |
| Fe[III] on D | UNIMOD:1870 | 18 |
| Dimethylation on K | UNIMOD:36 | 17 |
| Malonylation on K | UNIMOD:747 | 14 |
| Calcium on D | UNIMOD:951 | 13 |
| Carboxylation on E | UNIMOD:299 | 13 |
| Formylation on K | UNIMOD:122 | 13 |
| HexNAc on T | UNIMOD:43 | 12 |
| Potassium on D | UNIMOD:530 | 12 |
| N-acetylthreonine on T | UNIMOD:1 | 11 |
| Omega-N-methylarginine on R | UNIMOD:34 | 11 |
| Phosphothreonine on T | UNIMOD:21 | 11 |
| N6-succinyllysine on K | — | 10 |
| Calcium on E | UNIMOD:951 | 9 |
| 4-hydroxyproline on P | UNIMOD:35 | 8 |
| Carbamyl on K | UNIMOD:5 | 8 |
| Carboxylation on D | UNIMOD:299 | 7 |
| Dimethylation on R | UNIMOD:36 | 7 |
| Carbamyl on R | UNIMOD:5 | 6 |
| Crotonylation on K | UNIMOD:1363 | 5 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 5 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 5 |
| Trimethylation on K | UNIMOD:37 | 5 |
| Carbamyl on C | UNIMOD:5 | 4 |
| Glutarylation on K | UNIMOD:1848 | 4 |
| Nitrosylation on Y | UNIMOD:354 | 4 |
| Phosphotyrosine on Y | UNIMOD:21 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Carboxylation on K | UNIMOD:299 | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| Potassium on E | UNIMOD:530 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 2 |
| Butyrylation on K | UNIMOD:1289 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Deamidated asparagine on N | UNIMOD:7 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| N-myristoyl glycine on G | UNIMOD:45 | 2 |
| N6-butyryllysine on K | UNIMOD:1289 | 2 |
| Succinylation on K | UNIMOD:64 | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-carboxyglutamate on E | UNIMOD:299 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-methyllysine on K | UNIMOD:34 | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| Phosphorylation on Y | UNIMOD:21 | 1 |
| Sulfonation on Y | UNIMOD:40 | 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
ee32aa97b8585fc9, written 2026-10-29T09:09:42+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