Generated summary
PXD061069 is a DDA label-free dataset (Mus musculus) with 120 runs, 120 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 586,221 PSMs, 35,874 peptidoforms and 3,220 protein groups, and the repository holds 15,631 PTM sites for it. 8 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, 8 warnings and 1 for information
count_mismatch warning
The bundle holds 586221 where the producer reported 586385 (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 586221 where the producer reported 586385 (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
35.47% of protein intensity in the worst file, 3.99% median across 120 files (DEF-QC-9 v3.5)
35.47% of protein intensity in the worst file, 3.99% median across 120 files (DEF-QC-9 v3.5)
low_core_use warning
8.92 avg cores of 32 allowed (S5)
8.92 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: 586385/4095569 = 14.32% 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: 586385/4095569 = 14.32% of MS2 identified (S3)
occupancy_not_stored warning
Of 363666 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 10863 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 363666 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 10863 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).
peptide_rows_localization_ambiguous warning
253 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 1160 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `AAASAQTSSAVETLPMM[Common Variable:Oxidation on M]PPQSAPIQPK|AAASAQTSSAVETLPM[Common Variable:Oxidation on M]MPPQSAPIQPK`, `AAGGAKRK[Common Biological:Malonylation on K]TSGPPVSELIT[Common Biological:HexNAc on T]K|AAGGAKRK[Common Biological:Malonylation on K]TS[Common Biological:HexNAc on S]GPPVSELITK|AAGGAKRK[Common Biological:Malonylation on K]T[Common Biological:HexNAc on T]SGPPVSELITK`, `AANN[Common Artifact:Deamidation on N]GALPPDLSYIVR|AAN[Common Artifact:Deamidation on N]NGALPPDLSYIVR`.
253 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 1160 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `AAASAQTSSAVETLPMM[Common Variable:Oxidation on M]PPQSAPIQPK|AAASAQTSSAVETLPM[Common Variable:Oxidation on M]MPPQSAPIQPK`, `AAGGAKRK[Common Biological:Malonylation on K]TSGPPVSELIT[Common Biological:HexNAc on T]K|AAGGAKRK[Common Biological:Malonylation on K]TS[Common Biological:HexNAc on S]GPPVSELITK|AAGGAKRK[Common Biological:Malonylation on K]T[Common Biological:HexNAc on T]SGPPVSELITK`, `AANN[Common Artifact:Deamidation on N]GALPPDLSYIVR|AAN[Common Artifact:Deamidation on N]NGALPPDLSYIVR`.
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: Cell culture. 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: Cell culture. 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: 682 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: 682 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
75 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
75 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 | 586,221 |
| Peptidoforms at 1% FDR | 35,874 |
| Protein groups at 1% FDR | 3,220 |
| PTM sites | 15,631 |
| Quantitative values | 1,499,412 |
| PSMs, all (including decoys and sub-threshold) | 1,854,054 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 14.3% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 8.3% |
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
- proximity_labelling
- Instrument vendor
- Thermo
- Runs / samples
- 120 / 120
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.13
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v6.xml
- Pipeline commit
- 314f6ae55a6e
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 5,483 |
| Carbamidomethyl on C | UNIMOD:4 | 5,468 |
| Deamidation on N | UNIMOD:7 | 583 |
| Deamidation on Q | UNIMOD:7 | 389 |
| Phosphoserine on S | UNIMOD:21 | 375 |
| N-acetylalanine on A | UNIMOD:1 | 191 |
| Hydroxylation on P | UNIMOD:35 | 185 |
| Hydroxylation on K | UNIMOD:35 | 160 |
| Acetylation on X | UNIMOD:1 | 146 |
| Ammonia loss on N | UNIMOD:385 | 130 |
| Ammonia loss on C | UNIMOD:385 | 120 |
| N6-acetyllysine on K | UNIMOD:1 | 117 |
| Acetylation on K | UNIMOD:1 | 100 |
| Hydroxylation on N | UNIMOD:35 | 97 |
| N-acetylmethionine on M | UNIMOD:1 | 89 |
| Formylation on K | UNIMOD:122 | 87 |
| Phosphorylation on S | UNIMOD:21 | 84 |
| N-acetylserine on S | UNIMOD:1 | 70 |
| Methylation on K | UNIMOD:34 | 63 |
| Phosphothreonine on T | UNIMOD:21 | 57 |
| Carbamyl on X | UNIMOD:5 | 54 |
| Citrullination on R | UNIMOD:7 | 54 |
| Water Loss on E | UNIMOD:27 | 52 |
| Phosphorylation on T | UNIMOD:21 | 47 |
| N6-methyllysine on K | UNIMOD:34 | 46 |
| Sodium on E | UNIMOD:30 | 43 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 34 |
| Carbamyl on K | UNIMOD:5 | 33 |
| Carbamyl on M | UNIMOD:5 | 29 |
| Fe[III] on D | UNIMOD:1870 | 29 |
| HexNAc on T | UNIMOD:43 | 29 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 27 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 27 |
| Carboxylation on K | UNIMOD:299 | 25 |
| Methylation on R | UNIMOD:34 | 25 |
| Omega-N-methylarginine on R | UNIMOD:34 | 25 |
| N6-glutaryllysine on K | — | 23 |
| Dimethylation on R | UNIMOD:36 | 22 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 22 |
| N6-butyryllysine on K | UNIMOD:1289 | 21 |
| Sodium on D | UNIMOD:30 | 20 |
| Fe[III] on E | UNIMOD:1870 | 19 |
| 4-hydroxyproline on P | UNIMOD:35 | 18 |
| Calcium on E | UNIMOD:951 | 18 |
| Dimethylation on K | UNIMOD:36 | 18 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 18 |
| N-acetylthreonine on T | UNIMOD:1 | 18 |
| Trimethylation on K | UNIMOD:37 | 17 |
| Calcium on D | UNIMOD:951 | 16 |
| HexNAc on S | UNIMOD:43 | 16 |
| N6-succinyllysine on K | — | 15 |
| Potassium on E | UNIMOD:530 | 15 |
| Butyrylation on K | UNIMOD:1289 | 13 |
| Deamidated asparagine on N | UNIMOD:7 | 13 |
| Fe[II] on E | UNIMOD:952 | 13 |
| Malonylation on K | UNIMOD:747 | 13 |
| Succinylation on K | UNIMOD:64 | 13 |
| Phosphorylation on Y | UNIMOD:21 | 12 |
| Magnesium on E | UNIMOD:956 | 11 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 11 |
| N6-methacryllysine on K | — | 11 |
| Hydroxybutyrylation on K | — | 10 |
| Crotonylation on K | UNIMOD:1363 | 9 |
| Fe[II] on D | UNIMOD:952 | 9 |
| Carboxylation on D | UNIMOD:299 | 8 |
| Dimethylated arginine on R | UNIMOD:36 | 8 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 7 |
| Magnesium on D | UNIMOD:956 | 6 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| N6-crotonyllysine on K | — | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 6 |
| Potassium on D | UNIMOD:530 | 6 |
| Glutarylation on K | UNIMOD:1848 | 5 |
| Carboxylation on E | UNIMOD:299 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Citrulline on R | UNIMOD:7 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N6-benzoyllysine on K | UNIMOD:136 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N-myristoyl glycine on G | UNIMOD:45 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-propionyllysine on K | UNIMOD:58 | 2 |
| (3R)-3-hydroxyasparagine on N | UNIMOD:35 | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| Carbamyl on R | UNIMOD:5 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| Nitrosylation on Y | UNIMOD:354 | 1 |
| Propionamide on C | — | 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
aa28004db6dc8c3b, written 2026-10-31T17:48:39+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