Generated summary
PXD047288 is a DDA label-free dataset (Rattus norvegicus) with 36 runs, 36 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 8,398 PSMs, 884 peptidoforms and 367 protein groups, and the repository holds 1,602 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 1 for information
cysteine_poor warning
1.77% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
1.77% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
high_contamination warning
83.92% of protein intensity in the worst file, 61.88% median across 36 files (DEF-QC-9 v3.5)
83.92% of protein intensity in the worst file, 61.88% median across 36 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: 8398/712536 = 1.18% 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: 8398/712536 = 1.18% of MS2 identified (S3)
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 12834 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 240 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 12834 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 240 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: 115 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: 115 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
81 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
81 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 | 8,398 |
| Peptidoforms at 1% FDR | 884 |
| Protein groups at 1% FDR | 367 |
| PTM sites | 1,602 |
| Quantitative values | 51,704 |
| PSMs, all (including decoys and sub-threshold) | 372,505 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 1.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 77.0% |
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
- 36 / 36
- Sample metadata
- absent
- 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 |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 277 |
| Citrullination on R | UNIMOD:7 | 44 |
| Deamidation on N | UNIMOD:7 | 39 |
| Nethylmaleimide on C | UNIMOD:108 | 38 |
| Hydroxylation on P | UNIMOD:35 | 31 |
| Deamidation on Q | UNIMOD:7 | 27 |
| 4-hydroxyproline on P | UNIMOD:35 | 19 |
| Ammonia loss on N | UNIMOD:385 | 16 |
| Methylation on K | UNIMOD:34 | 12 |
| Dimethylation on R | UNIMOD:36 | 9 |
| HexNAc on S | UNIMOD:43 | 9 |
| Methylation on R | UNIMOD:34 | 8 |
| Hydroxylation on N | UNIMOD:35 | 7 |
| Acetylation on X | UNIMOD:1 | 6 |
| Dimethylation on K | UNIMOD:36 | 6 |
| Hydroxylation on K | UNIMOD:35 | 6 |
| N-acetylalanine on A | UNIMOD:1 | 6 |
| Phosphoserine on S | UNIMOD:21 | 6 |
| Carbamyl on K | UNIMOD:5 | 5 |
| Fe[II] on E | UNIMOD:952 | 5 |
| Formylation on K | UNIMOD:122 | 5 |
| Phosphorylation on S | UNIMOD:21 | 5 |
| Acetylation on K | UNIMOD:1 | 4 |
| Butyrylation on K | UNIMOD:1289 | 4 |
| HexNAc on T | UNIMOD:43 | 4 |
| Magnesium on D | UNIMOD:956 | 4 |
| Magnesium on E | UNIMOD:956 | 4 |
| N6-acetyllysine on K | UNIMOD:1 | 4 |
| Carbamyl on X | UNIMOD:5 | 3 |
| Fe[III] on E | UNIMOD:1870 | 3 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 3 |
| Sodium on D | UNIMOD:30 | 3 |
| Trimethylation on K | UNIMOD:37 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carboxylation on E | UNIMOD:299 | 2 |
| Glutarylation on K | UNIMOD:1848 | 2 |
| N-acetylmethionine on M | UNIMOD:1 | 2 |
| N-acetylserine on S | UNIMOD:1 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N6-methyllysine on K | UNIMOD:34 | 2 |
| Sulfonation on Y | UNIMOD:40 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| Water Loss on E | UNIMOD:27 | 2 |
| Ammonia loss on C | UNIMOD:385 | 1 |
| Calcium on E | UNIMOD:951 | 1 |
| Carboxylation on D | UNIMOD:299 | 1 |
| Carboxylation on K | UNIMOD:299 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Deamidated asparagine on N | UNIMOD:7 | 1 |
| Fe[III] on D | UNIMOD:1870 | 1 |
| N-acetylglycine on G | UNIMOD:1 | 1 |
| N-acetylthreonine on T | UNIMOD:1 | 1 |
| N6-succinyllysine on K | — | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| Omega-N-methylarginine on R | UNIMOD:34 | 1 |
| Phosphorylation on T | UNIMOD:21 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 1 |
| Potassium on D | UNIMOD:530 | 1 |
| Potassium on E | UNIMOD:530 | 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
3fb04088ea35c6e5, written 2026-10-29T09:26:50+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