Generated summary
PXD051203 is a DDA label-free dataset (Rattus norvegicus) with 39 runs, 20 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 34,103 PSMs, 3,649 peptidoforms and 921 protein groups, and the repository holds 2,133 PTM sites for it. 6 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, 6 warnings and 2 for information
cysteine_poor warning
1.68% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
1.68% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
high_contamination warning
50.60% of protein intensity in the worst file, 50.60% median across 1 files (DEF-QC-9 v3.5)
50.60% of protein intensity in the worst file, 50.60% median across 1 files (DEF-QC-9 v3.5)
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: 34103/613377 = 5.56% 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: 34103/613377 = 5.56% of MS2 identified (S3)
occupancy_not_stored warning
Of 12606 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 389 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 12606 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 389 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_skeleton warning
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
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: 165 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: 165 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.
excluded_from_search info
The deposited file 240301_JaromeFemaleRSC_A5_02.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: f4f31154ab874df1927de64e68c58aff8109a154fd3651399614fc6b5ac6f6e1.
The deposited file 240301_JaromeFemaleRSC_A5_02.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: f4f31154ab874df1927de64e68c58aff8109a154fd3651399614fc6b5ac6f6e1.
occupancy_decoy_groups info
18 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
18 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 | 34,103 |
| Peptidoforms at 1% FDR | 3,649 |
| Protein groups at 1% FDR | 921 |
| PTM sites | 2,133 |
| Quantitative values | 72,170 |
| PSMs, all (including decoys and sub-threshold) | 196,016 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 5.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 41.3% |
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
- affinity_purification
- Instrument vendor
- not recorded
- Runs / samples
- 39 / 20
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000002494_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 2b4533e54e28
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 438 |
| Deamidation on N | UNIMOD:7 | 144 |
| Nethylmaleimide on C | UNIMOD:108 | 111 |
| Deamidation on Q | UNIMOD:7 | 51 |
| Hydroxylation on P | UNIMOD:35 | 49 |
| Ammonia loss on N | UNIMOD:385 | 32 |
| Phosphoserine on S | UNIMOD:21 | 30 |
| N-acetylalanine on A | UNIMOD:1 | 22 |
| Fe[III] on E | UNIMOD:1870 | 21 |
| Citrullination on R | UNIMOD:7 | 19 |
| Hydroxylation on N | UNIMOD:35 | 16 |
| 4-hydroxyproline on P | UNIMOD:35 | 15 |
| Acetylation on X | UNIMOD:1 | 12 |
| Fe[II] on E | UNIMOD:952 | 12 |
| Phosphothreonine on T | UNIMOD:21 | 11 |
| N6-acetyllysine on K | UNIMOD:1 | 10 |
| Acetylation on K | UNIMOD:1 | 9 |
| Calcium on E | UNIMOD:951 | 9 |
| Methylation on K | UNIMOD:34 | 8 |
| N-acetylserine on S | UNIMOD:1 | 8 |
| Fe[II] on D | UNIMOD:952 | 7 |
| Hydroxylation on K | UNIMOD:35 | 7 |
| Carbamyl on X | UNIMOD:5 | 6 |
| N-acetylmethionine on M | UNIMOD:1 | 6 |
| Water Loss on E | UNIMOD:27 | 5 |
| Dimethylation on K | UNIMOD:36 | 4 |
| Dimethylation on R | UNIMOD:36 | 4 |
| Formylation on K | UNIMOD:122 | 4 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 4 |
| Omega-N-methylarginine on R | UNIMOD:34 | 4 |
| Sodium on E | UNIMOD:30 | 4 |
| Crotonylation on K | UNIMOD:1363 | 3 |
| Deamidated asparagine on N | UNIMOD:7 | 3 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 3 |
| N-acetylthreonine on T | UNIMOD:1 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| Phosphorylation on S | UNIMOD:21 | 3 |
| Phosphorylation on T | UNIMOD:21 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carbamyl on K | UNIMOD:5 | 2 |
| Carbamyl on R | UNIMOD:5 | 2 |
| Fe[III] on D | UNIMOD:1870 | 2 |
| Glutarylation on K | UNIMOD:1848 | 2 |
| Magnesium on E | UNIMOD:956 | 2 |
| Methylation on R | UNIMOD:34 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| N6-methyllysine on K | UNIMOD:34 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Calcium on D | UNIMOD:951 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Hydroxybutyrylation on K | — | 1 |
| Magnesium on D | UNIMOD:956 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 1 |
| N6-succinyllysine on K | — | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| Succinylation on K | UNIMOD:64 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Tele-methylhistidine on H | UNIMOD:34 | 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
d4f30604e10ff8a1, written 2026-10-29T09:40:12+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