Generated summary
PXD018315 is a DDA label-free dataset (Mus musculus) with 40 runs, 40 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 79,679 PSMs, 7,674 peptidoforms and 1,442 protein groups, and the repository holds 5,147 PTM sites for it. 4 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, 4 warnings and 2 for information
high_contamination warning
59.09% of protein intensity in the worst file, 24.30% median across 40 files (DEF-QC-9 v3.5)
59.09% of protein intensity in the worst file, 24.30% median across 40 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 23692 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1361 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 23692 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1361 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: 348 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: 348 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. PXD018315:A2AK42;A2AK44;Q8C5N3 written 2 times; quant_values: 40 identifier(s), 40 row(s) dropped, e.g. PXD018315:P18_063_JuliaT_pd26_Ctrl_01:label_free:protein_group:PXD018315:A2AK42;A2AK44;Q8C5N3: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: 1 identifier(s), 1 row(s) dropped, e.g. PXD018315:A2AK42;A2AK44;Q8C5N3 written 2 times; quant_values: 40 identifier(s), 40 row(s) dropped, e.g. PXD018315:P18_063_JuliaT_pd26_Ctrl_01:label_free:protein_group:PXD018315:A2AK42;A2AK44;Q8C5N3:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
30 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
30 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 | 79,679 |
| Peptidoforms at 1% FDR | 7,674 |
| Protein groups at 1% FDR | 1,442 |
| PTM sites | 5,147 |
| Quantitative values | 252,376 |
| PSMs, all (including decoys and sub-threshold) | 275,348 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 18.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 17.7% |
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
- affinity_purification
- Instrument vendor
- not recorded
- Runs / samples
- 40 / 40
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 2eb9a52d7f0c
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 1,298 |
| Oxidation on M | UNIMOD:35 | 1,063 |
| Deamidation on N | UNIMOD:7 | 276 |
| Hydroxylation on P | UNIMOD:35 | 136 |
| Deamidation on Q | UNIMOD:7 | 126 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 89 |
| Hydroxylation on N | UNIMOD:35 | 80 |
| Carbamyl on X | UNIMOD:5 | 79 |
| Hydroxylation on K | UNIMOD:35 | 66 |
| Carbamyl on M | UNIMOD:5 | 64 |
| N-acetylalanine on A | UNIMOD:1 | 51 |
| Acetylation on K | UNIMOD:1 | 48 |
| Formylation on K | UNIMOD:122 | 48 |
| Phosphoserine on S | UNIMOD:21 | 48 |
| Methylation on K | UNIMOD:34 | 45 |
| Ammonia loss on N | UNIMOD:385 | 43 |
| Glutarylation on K | UNIMOD:1848 | 40 |
| Ammonia loss on C | UNIMOD:385 | 36 |
| Citrullination on R | UNIMOD:7 | 35 |
| Methylation on R | UNIMOD:34 | 35 |
| Sodium on D | UNIMOD:30 | 24 |
| N6-acetyllysine on K | UNIMOD:1 | 22 |
| N-acetylserine on S | UNIMOD:1 | 21 |
| Fe[III] on D | UNIMOD:1870 | 19 |
| Carboxylation on D | UNIMOD:299 | 18 |
| Fe[II] on D | UNIMOD:952 | 18 |
| Sodium on E | UNIMOD:30 | 18 |
| Fe[II] on E | UNIMOD:952 | 17 |
| Calcium on D | UNIMOD:951 | 16 |
| Acetylation on X | UNIMOD:1 | 15 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 15 |
| Carbamyl on K | UNIMOD:5 | 15 |
| Fe[III] on E | UNIMOD:1870 | 15 |
| N-acetylmethionine on M | UNIMOD:1 | 15 |
| Trimethylation on K | UNIMOD:37 | 13 |
| Dimethylation on K | UNIMOD:36 | 10 |
| N-acetylthreonine on T | UNIMOD:1 | 10 |
| Phosphorylation on S | UNIMOD:21 | 10 |
| Carboxylation on E | UNIMOD:299 | 9 |
| Potassium on D | UNIMOD:530 | 9 |
| Carbamyl on R | UNIMOD:5 | 8 |
| Hydroxybutyrylation on K | — | 8 |
| Omega-N-methylarginine on R | UNIMOD:34 | 8 |
| Calcium on E | UNIMOD:951 | 7 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 7 |
| Phosphorylation on T | UNIMOD:21 | 7 |
| Phosphothreonine on T | UNIMOD:21 | 7 |
| Potassium on E | UNIMOD:530 | 7 |
| Malonylation on K | UNIMOD:747 | 6 |
| Water Loss on E | UNIMOD:27 | 6 |
| Carboxylation on K | UNIMOD:299 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 5 |
| Magnesium on D | UNIMOD:956 | 5 |
| Magnesium on E | UNIMOD:956 | 5 |
| Phosphorylation on Y | UNIMOD:21 | 5 |
| Succinylation on K | UNIMOD:64 | 5 |
| Sulfonation on Y | UNIMOD:40 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Butyrylation on K | UNIMOD:1289 | 4 |
| Carbamyl on C | UNIMOD:5 | 4 |
| Nitrosylation on Y | UNIMOD:354 | 4 |
| Crotonylation on K | UNIMOD:1363 | 3 |
| Dimethylation on R | UNIMOD:36 | 3 |
| HexNAc on S | UNIMOD:43 | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| N6-methyllysine on K | UNIMOD:34 | 3 |
| N6-succinyllysine on K | — | 3 |
| 4-carboxyglutamate on E | UNIMOD:299 | 2 |
| 4-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 2 |
| N6-methacryllysine on K | — | 2 |
| Nitrosylation on C | UNIMOD:275 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| HexNAc on T | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
4e3e088202b5c3b0, written 2026-10-29T09:32:16+00:00 by ingester 1.4.0- Reconciliation
- every check agreed with the producer's own counts
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group