Generated summary
PXD024633 is a DDA label-free dataset (Mus musculus) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 667,123 PSMs, 37,083 peptidoforms and 3,006 protein groups, and the repository holds 14,203 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 667123 where the producer reported 667163 (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 667123 where the producer reported 667163 (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 111511 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4393 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 111511 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4393 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
575 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 1061 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. `AALSAGK[Common Biological:Methylation on K]VPP[Common Biological:Hydroxylation on P]ETIDSVIVGNVMQSSSDAAYLAR|AALSAGK[Common Biological:Methylation on K]VP[Common Biological:Hydroxylation on P]PETIDSVIVGNVMQSSSDAAYLAR`, `AANEAGYFNEE[Metal:Fe[III] on E]M[Common Variable:Oxidation on M]APIEVK|AANEAGYFNE[Metal:Fe[III] on E]EM[Common Variable:Oxidation on M]APIEVK`, `AANEAGYFNEE[Metal:Magnesium on E]M[Common Variable:Oxidation on M]APIEVK|AANEAGYFNE[Metal:Magnesium on E]EM[Common Variable:Oxidation on M]APIEVK`.
575 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 1061 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. `AALSAGK[Common Biological:Methylation on K]VPP[Common Biological:Hydroxylation on P]ETIDSVIVGNVMQSSSDAAYLAR|AALSAGK[Common Biological:Methylation on K]VP[Common Biological:Hydroxylation on P]PETIDSVIVGNVMQSSSDAAYLAR`, `AANEAGYFNEE[Metal:Fe[III] on E]M[Common Variable:Oxidation on M]APIEVK|AANEAGYFNE[Metal:Fe[III] on E]EM[Common Variable:Oxidation on M]APIEVK`, `AANEAGYFNEE[Metal:Magnesium on E]M[Common Variable:Oxidation on M]APIEVK|AANEAGYFNE[Metal:Magnesium on E]EM[Common Variable:Oxidation on M]APIEVK`.
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. 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. 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: 2919 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: 2919 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
68 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
68 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 | 667,123 |
| Peptidoforms at 1% FDR | 37,083 |
| Protein groups at 1% FDR | 3,006 |
| PTM sites | 14,203 |
| Quantitative values | 308,698 |
| PSMs, all (including decoys and sub-threshold) | 1,669,381 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 39.8% |
| 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
- none
- Instrument vendor
- Thermo
- Runs / samples
- 10 / 10
- 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 |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 3,285 |
| Oxidation on M | UNIMOD:35 | 2,975 |
| Formylation on K | UNIMOD:122 | 1,006 |
| Deamidation on N | UNIMOD:7 | 627 |
| Deamidation on Q | UNIMOD:7 | 522 |
| Fe[III] on E | UNIMOD:1870 | 390 |
| Ammonia loss on N | UNIMOD:385 | 306 |
| Fe[II] on E | UNIMOD:952 | 295 |
| Fe[III] on D | UNIMOD:1870 | 244 |
| Fe[II] on D | UNIMOD:952 | 241 |
| Methylation on K | UNIMOD:34 | 224 |
| Sodium on E | UNIMOD:30 | 209 |
| N6-acetyllysine on K | UNIMOD:1 | 206 |
| N-acetylalanine on A | UNIMOD:1 | 169 |
| Hydroxylation on P | UNIMOD:35 | 164 |
| Acetylation on X | UNIMOD:1 | 162 |
| Magnesium on E | UNIMOD:956 | 141 |
| Sodium on D | UNIMOD:30 | 140 |
| Phosphoserine on S | UNIMOD:21 | 128 |
| Acetylation on K | UNIMOD:1 | 117 |
| Calcium on E | UNIMOD:951 | 113 |
| Ammonia loss on C | UNIMOD:385 | 108 |
| Calcium on D | UNIMOD:951 | 104 |
| Citrullination on R | UNIMOD:7 | 101 |
| Magnesium on D | UNIMOD:956 | 100 |
| Hydroxylation on K | UNIMOD:35 | 99 |
| Dimethylation on K | UNIMOD:36 | 95 |
| Water Loss on E | UNIMOD:27 | 94 |
| Hydroxylation on N | UNIMOD:35 | 81 |
| N6-succinyllysine on K | — | 81 |
| Phosphorylation on S | UNIMOD:21 | 81 |
| Trimethylation on K | UNIMOD:37 | 81 |
| Methylation on R | UNIMOD:34 | 78 |
| Carbamyl on X | UNIMOD:5 | 75 |
| N-acetylserine on S | UNIMOD:1 | 72 |
| Potassium on E | UNIMOD:530 | 72 |
| N-acetylmethionine on M | UNIMOD:1 | 67 |
| Potassium on D | UNIMOD:530 | 58 |
| Dimethylation on R | UNIMOD:36 | 49 |
| HexNAc on T | UNIMOD:43 | 44 |
| HexNAc on S | UNIMOD:43 | 39 |
| Phosphorylation on T | UNIMOD:21 | 39 |
| Succinylation on K | UNIMOD:64 | 36 |
| Malonylation on K | UNIMOD:747 | 33 |
| 4-hydroxyproline on P | UNIMOD:35 | 32 |
| Crotonylation on K | UNIMOD:1363 | 31 |
| Hydroxybutyrylation on K | — | 30 |
| Omega-N-methylarginine on R | UNIMOD:34 | 30 |
| Carboxylation on K | UNIMOD:299 | 29 |
| Nitrosylation on Y | UNIMOD:354 | 28 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 27 |
| Carboxylation on D | UNIMOD:299 | 25 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 24 |
| Carboxylation on E | UNIMOD:299 | 24 |
| Butyrylation on K | UNIMOD:1289 | 22 |
| N6-methyllysine on K | UNIMOD:34 | 21 |
| Carbamyl on K | UNIMOD:5 | 20 |
| N-acetylthreonine on T | UNIMOD:1 | 19 |
| N6-crotonyllysine on K | — | 19 |
| Glutarylation on K | UNIMOD:1848 | 18 |
| Phosphothreonine on T | UNIMOD:21 | 18 |
| Deamidated asparagine on N | UNIMOD:7 | 17 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 16 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 14 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 14 |
| Nitrosylation on C | UNIMOD:275 | 12 |
| Carbamyl on M | UNIMOD:5 | 11 |
| Cu[I] on E | UNIMOD:531 | 11 |
| Phosphorylation on Y | UNIMOD:21 | 11 |
| Phosphotyrosine on Y | UNIMOD:21 | 7 |
| Zinc on E | UNIMOD:954 | 7 |
| 5-hydroxylysine on K | UNIMOD:35 | 6 |
| Carbamyl on R | UNIMOD:5 | 5 |
| Citrulline on R | UNIMOD:7 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Cu[I] on D | UNIMOD:531 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| Allysine on K | UNIMOD:352 | 3 |
| Glu to PyroGlu on Q | UNIMOD:28 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 3 |
| N6-butyryllysine on K | UNIMOD:1289 | 3 |
| N6-glutaryllysine on K | — | 3 |
| N6-methacryllysine on K | — | 3 |
| N6-propionyllysine on K | UNIMOD:58 | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| (3S)-3-hydroxyasparagine on N | — | 2 |
| Carbamyl on C | UNIMOD:5 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| N-myristoyl glycine on G | UNIMOD:45 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N,N,N-trimethylalanine on A | UNIMOD:37 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 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
1e9e0279bff99a53, written 2026-11-01T20:54:52+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