Generated summary
PXD022196 is a DDA label-free dataset (Mus musculus) with 32 runs, 4 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 250,902 PSMs, 26,178 peptidoforms and 3,800 protein groups, and the repository holds 13,517 PTM sites for it. 6 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, 6 warnings and 2 for information
count_mismatch warning
The bundle holds 250902 where the producer reported 250985 (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 250902 where the producer reported 250985 (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.
low_core_use warning
15.78 avg cores of 32 allowed (S5)
15.78 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: 250985/1715551 = 14.63% 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: 250985/1715551 = 14.63% of MS2 identified (S3)
occupancy_not_stored warning
Of 18043 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1792 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 18043 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1792 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_skeleton warning
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
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: 1330 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: 1330 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), 1 row(s) dropped, e.g. PXD022196:A0A087WR13;A0A571BD48 written 2 times; quant_values: 7 identifier(s), 7 row(s) dropped, e.g. PXD022196:design:5-K0_1:protein_group:PXD022196:A0A087WR13;A0A571BD48:QuantProject:DEF-PROT-INT written 2 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), 1 row(s) dropped, e.g. PXD022196:A0A087WR13;A0A571BD48 written 2 times; quant_values: 7 identifier(s), 7 row(s) dropped, e.g. PXD022196:design:5-K0_1:protein_group:PXD022196:A0A087WR13;A0A571BD48:QuantProject:DEF-PROT-INT written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
35 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
35 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 | 250,902 |
| Peptidoforms at 1% FDR | 26,178 |
| Protein groups at 1% FDR | 3,800 |
| PTM sites | 13,517 |
| Quantitative values | 164,892 |
| PSMs, all (including decoys and sub-threshold) | 461,653 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 14.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 16.3% |
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
- 32 / 4
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 6ea39b9e1b3a
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 4,967 |
| Oxidation on M | UNIMOD:35 | 1,650 |
| Deamidation on N | UNIMOD:7 | 1,139 |
| Deamidation on Q | UNIMOD:7 | 783 |
| Hydroxylation on P | UNIMOD:35 | 400 |
| Fe[III] on E | UNIMOD:1870 | 360 |
| Fe[III] on D | UNIMOD:1870 | 303 |
| Carbamyl on X | UNIMOD:5 | 258 |
| Fe[II] on E | UNIMOD:952 | 182 |
| N-acetylalanine on A | UNIMOD:1 | 168 |
| Citrullination on R | UNIMOD:7 | 161 |
| Hydroxylation on N | UNIMOD:35 | 160 |
| Fe[II] on D | UNIMOD:952 | 136 |
| Acetylation on K | UNIMOD:1 | 134 |
| Ammonia loss on N | UNIMOD:385 | 109 |
| Hydroxylation on K | UNIMOD:35 | 109 |
| Acetylation on X | UNIMOD:1 | 93 |
| Phosphoserine on S | UNIMOD:21 | 87 |
| Ammonia loss on C | UNIMOD:385 | 81 |
| N-acetylmethionine on M | UNIMOD:1 | 78 |
| Formylation on K | UNIMOD:122 | 77 |
| Methylation on K | UNIMOD:34 | 72 |
| N-acetylserine on S | UNIMOD:1 | 68 |
| N6-acetyllysine on K | UNIMOD:1 | 61 |
| Methylation on R | UNIMOD:34 | 47 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 40 |
| Carbamyl on M | UNIMOD:5 | 39 |
| Sodium on E | UNIMOD:30 | 34 |
| N6-methyllysine on K | UNIMOD:34 | 30 |
| Carboxylation on D | UNIMOD:299 | 28 |
| Calcium on D | UNIMOD:951 | 27 |
| Omega-N-methylarginine on R | UNIMOD:34 | 24 |
| Magnesium on D | UNIMOD:956 | 21 |
| Carbamyl on K | UNIMOD:5 | 20 |
| Carboxylation on E | UNIMOD:299 | 19 |
| 4-hydroxyproline on P | UNIMOD:35 | 18 |
| Dimethylation on R | UNIMOD:36 | 18 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 17 |
| Dimethylation on K | UNIMOD:36 | 17 |
| Phosphorylation on T | UNIMOD:21 | 17 |
| Calcium on E | UNIMOD:951 | 16 |
| N-acetylthreonine on T | UNIMOD:1 | 16 |
| Phosphothreonine on T | UNIMOD:21 | 16 |
| Deamidated asparagine on N | UNIMOD:7 | 15 |
| N6-glutaryllysine on K | — | 15 |
| HexNAc on T | UNIMOD:43 | 14 |
| N5-methylglutamine on Q | UNIMOD:34 | 14 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 14 |
| Sodium on D | UNIMOD:30 | 14 |
| Trimethylation on K | UNIMOD:37 | 14 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 10 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 10 |
| Magnesium on E | UNIMOD:956 | 9 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 9 |
| Carbamyl on R | UNIMOD:5 | 8 |
| Nitrosylation on Y | UNIMOD:354 | 8 |
| Phosphorylation on S | UNIMOD:21 | 8 |
| Potassium on D | UNIMOD:530 | 6 |
| Potassium on E | UNIMOD:530 | 6 |
| Carbamyl on C | UNIMOD:5 | 5 |
| Phosphorylation on Y | UNIMOD:21 | 5 |
| Water Loss on E | UNIMOD:27 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N-myristoyl glycine on G | UNIMOD:45 | 4 |
| N6-butyryllysine on K | UNIMOD:1289 | 4 |
| Phosphotyrosine on Y | UNIMOD:21 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Butyrylation on K | UNIMOD:1289 | 3 |
| Glutarylation on K | UNIMOD:1848 | 3 |
| HexNAc on S | UNIMOD:43 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| N6-crotonyllysine on K | — | 3 |
| N6-propionyllysine on K | UNIMOD:58 | 3 |
| N6-succinyllysine on K | — | 3 |
| Sulfonation on Y | UNIMOD:40 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 4-carboxyglutamate on E | UNIMOD:299 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Allysine on K | UNIMOD:352 | 2 |
| Carboxylation on K | UNIMOD:299 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| Nitrosylation on C | UNIMOD:275 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| Malonylation on K | UNIMOD:747 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 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
487e71045925c9d9, written 2026-10-29T09:08:50+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