Generated summary
PXD034432 is a DDA label-free dataset (Rattus norvegicus) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 38,154 PSMs, 2,836 peptidoforms and 608 protein groups, and the repository holds 3,363 PTM sites for it. 7 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, 7 warnings and 1 for information
count_mismatch warning
The bundle holds 38154 where the producer reported 38196 (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 38154 where the producer reported 38196 (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
13.12% of protein intensity in the worst file, 8.05% median across 10 files (DEF-QC-9 v3.5)
13.12% of protein intensity in the worst file, 8.05% median across 10 files (DEF-QC-9 v3.5)
low_core_use warning
14.4 avg cores of 32 allowed (S5)
14.4 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: 38196/713218 = 5.36% 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: 38196/713218 = 5.36% of MS2 identified (S3)
occupancy_not_stored warning
Of 9370 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 86 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 9370 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 86 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: Urine. 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: Urine. 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: 607 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: 607 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
3 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
3 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 | 38,154 |
| Peptidoforms at 1% FDR | 2,836 |
| Protein groups at 1% FDR | 608 |
| PTM sites | 3,363 |
| Quantitative values | 41,709 |
| PSMs, all (including decoys and sub-threshold) | 82,340 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 5.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 7.5% |
How it was measured
- Organism searched
- Rattus norvegicus (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 1.1.12
- Protein database
- UP000002494_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 836 |
| Oxidation on M | UNIMOD:35 | 476 |
| Deamidation on N | UNIMOD:7 | 267 |
| Formylation on K | UNIMOD:122 | 127 |
| Deamidation on Q | UNIMOD:7 | 109 |
| Methylation on K | UNIMOD:34 | 86 |
| Hydroxylation on P | UNIMOD:35 | 81 |
| Ammonia loss on N | UNIMOD:385 | 78 |
| Hydroxylation on N | UNIMOD:35 | 76 |
| Carbamyl on X | UNIMOD:5 | 73 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 61 |
| Methylation on R | UNIMOD:34 | 61 |
| Citrullination on R | UNIMOD:7 | 53 |
| Acetylation on K | UNIMOD:1 | 46 |
| Hydroxylation on K | UNIMOD:35 | 46 |
| Ammonia loss on C | UNIMOD:385 | 43 |
| Carbamyl on M | UNIMOD:5 | 42 |
| Fe[III] on D | UNIMOD:1870 | 37 |
| Carbamyl on K | UNIMOD:5 | 35 |
| Glutarylation on K | UNIMOD:1848 | 33 |
| Calcium on E | UNIMOD:951 | 32 |
| Carboxylation on D | UNIMOD:299 | 29 |
| Magnesium on D | UNIMOD:956 | 25 |
| Fe[III] on E | UNIMOD:1870 | 24 |
| Carboxylation on E | UNIMOD:299 | 22 |
| Magnesium on E | UNIMOD:956 | 21 |
| Calcium on D | UNIMOD:951 | 19 |
| Carbamyl on R | UNIMOD:5 | 19 |
| Water Loss on E | UNIMOD:27 | 17 |
| Dimethylation on R | UNIMOD:36 | 15 |
| Fe[II] on D | UNIMOD:952 | 15 |
| Nitrosylation on Y | UNIMOD:354 | 15 |
| Trimethylation on K | UNIMOD:37 | 15 |
| Potassium on D | UNIMOD:530 | 13 |
| Sodium on D | UNIMOD:30 | 13 |
| Malonylation on K | UNIMOD:747 | 12 |
| Nitrosylation on C | UNIMOD:275 | 12 |
| HexNAc on S | UNIMOD:43 | 11 |
| Hydroxybutyrylation on K | — | 11 |
| Fe[II] on E | UNIMOD:952 | 10 |
| Sodium on E | UNIMOD:30 | 10 |
| Dimethylation on K | UNIMOD:36 | 9 |
| Phosphorylation on S | UNIMOD:21 | 9 |
| Succinylation on K | UNIMOD:64 | 9 |
| Butyrylation on K | UNIMOD:1289 | 8 |
| Carbamyl on C | UNIMOD:5 | 8 |
| 4-hydroxyproline on P | UNIMOD:35 | 7 |
| Glu to PyroGlu on Q | UNIMOD:28 | 6 |
| Phosphoserine on S | UNIMOD:21 | 5 |
| Acetylation on X | UNIMOD:1 | 4 |
| Crotonylation on K | UNIMOD:1363 | 4 |
| N-acetylalanine on A | UNIMOD:1 | 4 |
| N-acetylserine on S | UNIMOD:1 | 4 |
| Carboxylation on K | UNIMOD:299 | 3 |
| Deamidated asparagine on N | UNIMOD:7 | 3 |
| N6-acetyllysine on K | UNIMOD:1 | 2 |
| Potassium on E | UNIMOD:530 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| HexNAc on T | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylmethionine on M | UNIMOD:1 | 1 |
| N-acetylthreonine on T | UNIMOD:1 | 1 |
| N-acetylvaline on V | UNIMOD:1 | 1 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 1 |
| Omega-N-methylarginine on R | UNIMOD:34 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 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
24368f638148b497, written 2026-10-29T09:50:00+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