Generated summary
PXD021762 is a DDA label-free dataset (Mus musculus) with 33 runs, 33 samples and an enrichment step outside the controlled list (recorded as `other`). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 227,290 PSMs, 12,628 peptidoforms and 1,586 protein groups, and the repository holds 8,307 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 12629 where the producer reported 12628 (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 12629 where the producer reported 12628 (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 227290 where the producer reported 227293 (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 227290 where the producer reported 227293 (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.
occupancy_not_stored warning
Of 20416 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4267 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 20416 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4267 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_uncoded warning
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: heart, liver. Match on it as text; it has not been mapped to a term.
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: heart, liver. Match on it as text; it has not been mapped to a term.
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: 379 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: 379 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
42 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
42 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 | 227,290 |
| Peptidoforms at 1% FDR | 12,628 |
| Protein groups at 1% FDR | 1,586 |
| PTM sites | 8,307 |
| Quantitative values | 425,327 |
| PSMs, all (including decoys and sub-threshold) | 508,156 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 20.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.3% |
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
- other
- Instrument vendor
- Thermo
- Runs / samples
- 33 / 33
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 9df4ce025f23
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 2,260 |
| Oxidation on M | UNIMOD:35 | 1,514 |
| Deamidation on N | UNIMOD:7 | 1,074 |
| Deamidation on Q | UNIMOD:7 | 1,068 |
| Citrullination on R | UNIMOD:7 | 400 |
| Hydroxylation on P | UNIMOD:35 | 323 |
| Ammonia loss on N | UNIMOD:385 | 159 |
| Hydroxylation on K | UNIMOD:35 | 139 |
| Methylation on K | UNIMOD:34 | 103 |
| N-acetylalanine on A | UNIMOD:1 | 103 |
| Acetylation on X | UNIMOD:1 | 87 |
| Hydroxylation on N | UNIMOD:35 | 76 |
| Magnesium on E | UNIMOD:956 | 64 |
| N6-acetyllysine on K | UNIMOD:1 | 60 |
| Formylation on K | UNIMOD:122 | 53 |
| Magnesium on D | UNIMOD:956 | 51 |
| Sodium on E | UNIMOD:30 | 51 |
| N-acetylmethionine on M | UNIMOD:1 | 45 |
| N-acetylserine on S | UNIMOD:1 | 45 |
| Phosphoserine on S | UNIMOD:21 | 43 |
| Sodium on D | UNIMOD:30 | 43 |
| Methylation on R | UNIMOD:34 | 37 |
| Dimethylation on K | UNIMOD:36 | 35 |
| Ammonia loss on C | UNIMOD:385 | 31 |
| Acetylation on K | UNIMOD:1 | 30 |
| Trimethylation on K | UNIMOD:37 | 23 |
| N6-succinyllysine on K | — | 20 |
| Phosphorylation on T | UNIMOD:21 | 19 |
| Phosphorylation on S | UNIMOD:21 | 17 |
| Dimethylation on R | UNIMOD:36 | 16 |
| HexNAc on T | UNIMOD:43 | 13 |
| Malonylation on K | UNIMOD:747 | 12 |
| Succinylation on K | UNIMOD:64 | 12 |
| HexNAc on S | UNIMOD:43 | 11 |
| Hydroxybutyrylation on K | — | 11 |
| Carbamyl on X | UNIMOD:5 | 10 |
| N-acetylthreonine on T | UNIMOD:1 | 9 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 9 |
| Water Loss on E | UNIMOD:27 | 9 |
| Deamidated asparagine on N | UNIMOD:7 | 8 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 8 |
| 4-hydroxyproline on P | UNIMOD:35 | 7 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 7 |
| Butyrylation on K | UNIMOD:1289 | 7 |
| Omega-N-methylarginine on R | UNIMOD:34 | 7 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 6 |
| N6-methyllysine on K | UNIMOD:34 | 6 |
| Phosphothreonine on T | UNIMOD:21 | 6 |
| Crotonylation on K | UNIMOD:1363 | 5 |
| N6-methacryllysine on K | — | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Glutarylation on K | UNIMOD:1848 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| Phosphorylation on Y | UNIMOD:21 | 4 |
| N6-lipoyllysine on K | UNIMOD:42 | 3 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| Carbamyl on K | UNIMOD:5 | 2 |
| Carbamyl on M | UNIMOD:5 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-glutaryllysine on K | — | 2 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 2 |
| Nitrosylation on C | UNIMOD:275 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Carbamyl on R | UNIMOD:5 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-malonyllysine on K | — | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
c0f326d398c75b16, written 2026-10-29T11:22:27+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