Generated summary
PXD041766 is a DDA label-free dataset (Mus musculus) with 8 runs, 8 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 199,344 PSMs, 36,229 peptidoforms and 3,372 protein groups, and the repository holds 23,381 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 199344 where the producer reported 199405 (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 199344 where the producer reported 199405 (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
14.65% of protein intensity in the worst file, 10.78% median across 8 files (DEF-QC-9 v3.5)
14.65% of protein intensity in the worst file, 10.78% median across 8 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 87031 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2301 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 87031 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2301 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: 1931 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: 1931 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: 2 identifier(s), 2 row(s) dropped, e.g. PXD041766:A2AJK6;Q09XV5;Q8BYH8 written 2 times; quant_values: 16 identifier(s), 16 row(s) dropped, e.g. PXD041766:1_t3t_1:label_free:protein_group:PXD041766:A2AJK6;Q09XV5;Q8BYH8:QuantProject:DEF-PROT-SPC 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: 2 identifier(s), 2 row(s) dropped, e.g. PXD041766:A2AJK6;Q09XV5;Q8BYH8 written 2 times; quant_values: 16 identifier(s), 16 row(s) dropped, e.g. PXD041766:1_t3t_1:label_free:protein_group:PXD041766:A2AJK6;Q09XV5;Q8BYH8:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
90 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
90 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 | 199,344 |
| Peptidoforms at 1% FDR | 36,229 |
| Protein groups at 1% FDR | 3,372 |
| PTM sites | 23,381 |
| Quantitative values | 215,286 |
| PSMs, all (including decoys and sub-threshold) | 452,639 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 31.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 13.0% |
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
- 8 / 8
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- ef0213be9f73
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Deamidation on Q | UNIMOD:7 | 5,810 |
| Deamidation on N | UNIMOD:7 | 4,136 |
| Oxidation on M | UNIMOD:35 | 3,730 |
| Carbamidomethyl on C | UNIMOD:4 | 2,965 |
| Citrullination on R | UNIMOD:7 | 992 |
| Hydroxylation on P | UNIMOD:35 | 751 |
| Methylation on K | UNIMOD:34 | 419 |
| Hydroxylation on N | UNIMOD:35 | 391 |
| Hydroxylation on K | UNIMOD:35 | 322 |
| Methylation on R | UNIMOD:34 | 225 |
| N-acetylalanine on A | UNIMOD:1 | 165 |
| Ammonia loss on N | UNIMOD:385 | 120 |
| Magnesium on D | UNIMOD:956 | 89 |
| Acetylation on X | UNIMOD:1 | 85 |
| Magnesium on E | UNIMOD:956 | 78 |
| Carbamyl on X | UNIMOD:5 | 68 |
| N-acetylmethionine on M | UNIMOD:1 | 68 |
| Sodium on D | UNIMOD:30 | 67 |
| Dimethylation on K | UNIMOD:36 | 58 |
| Phosphoserine on S | UNIMOD:21 | 57 |
| N-acetylserine on S | UNIMOD:1 | 52 |
| Carbamyl on M | UNIMOD:5 | 50 |
| Sodium on E | UNIMOD:30 | 50 |
| N6-acetyllysine on K | UNIMOD:1 | 46 |
| Acetylation on K | UNIMOD:1 | 45 |
| Water Loss on E | UNIMOD:27 | 45 |
| Trimethylation on K | UNIMOD:37 | 42 |
| Carboxylation on E | UNIMOD:299 | 34 |
| Carboxylation on D | UNIMOD:299 | 33 |
| Ammonia loss on C | UNIMOD:385 | 32 |
| Formylation on K | UNIMOD:122 | 30 |
| Malonylation on K | UNIMOD:747 | 30 |
| Fe[II] on E | UNIMOD:952 | 29 |
| Calcium on E | UNIMOD:951 | 28 |
| Phosphorylation on T | UNIMOD:21 | 23 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 21 |
| Nitrosylation on C | UNIMOD:275 | 21 |
| Nitrosylation on Y | UNIMOD:354 | 20 |
| Deamidated asparagine on N | UNIMOD:7 | 19 |
| Fe[III] on E | UNIMOD:1870 | 19 |
| Phosphorylation on S | UNIMOD:21 | 19 |
| Fe[II] on D | UNIMOD:952 | 17 |
| Calcium on D | UNIMOD:951 | 16 |
| Dimethylation on R | UNIMOD:36 | 16 |
| HexNAc on T | UNIMOD:43 | 16 |
| Crotonylation on K | UNIMOD:1363 | 15 |
| Succinylation on K | UNIMOD:64 | 14 |
| Butyrylation on K | UNIMOD:1289 | 13 |
| Glutarylation on K | UNIMOD:1848 | 13 |
| Hydroxybutyrylation on K | — | 13 |
| N-myristoyl glycine on G | UNIMOD:45 | 13 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 12 |
| Fe[III] on D | UNIMOD:1870 | 12 |
| N-acetylthreonine on T | UNIMOD:1 | 11 |
| Carbamyl on C | UNIMOD:5 | 10 |
| HexNAc on S | UNIMOD:43 | 10 |
| N6-methyllysine on K | UNIMOD:34 | 10 |
| Phosphothreonine on T | UNIMOD:21 | 10 |
| Potassium on D | UNIMOD:530 | 10 |
| Carbamyl on K | UNIMOD:5 | 9 |
| Phosphorylation on Y | UNIMOD:21 | 9 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 8 |
| Omega-N-methylarginine on R | UNIMOD:34 | 8 |
| Potassium on E | UNIMOD:530 | 8 |
| Sulfonation on Y | UNIMOD:40 | 8 |
| Carboxylation on K | UNIMOD:299 | 7 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 6 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 6 |
| N6-glutaryllysine on K | — | 6 |
| Citrulline on R | UNIMOD:7 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| Phosphotyrosine on Y | UNIMOD:21 | 5 |
| 4-hydroxyproline on P | UNIMOD:35 | 4 |
| N6-succinyllysine on K | — | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Carbamyl on R | UNIMOD:5 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-propionyllysine on K | UNIMOD:58 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-malonyllysine on K | — | 1 |
| Pros-methylhistidine on H | 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
60c70d3b5376be88, written 2026-10-29T13:22:55+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