Generated summary
PXD056458 is a DDA label-free dataset (Rattus norvegicus) with 38 runs, 19 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 118,038 PSMs, 978 peptidoforms and 357 protein groups, and the repository holds 1,962 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 1 for information
cysteine_poor warning
3.91% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
3.91% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
occupancy_not_stored warning
Of 7398 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 388 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 7398 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 388 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: 622 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: 622 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
67 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
67 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 | 118,038 |
| Peptidoforms at 1% FDR | 978 |
| Protein groups at 1% FDR | 357 |
| PTM sites | 1,962 |
| Quantitative values | 56,963 |
| PSMs, all (including decoys and sub-threshold) | 377,717 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 24.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 36.0% |
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
- 38 / 19
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000002494_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 852cea5e1cd7
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 592 |
| Nethylmaleimide on C | UNIMOD:108 | 149 |
| Deamidation on N | UNIMOD:7 | 121 |
| Deamidation on Q | UNIMOD:7 | 112 |
| Hydroxylation on P | UNIMOD:35 | 68 |
| Hydroxylation on N | UNIMOD:35 | 50 |
| Citrullination on R | UNIMOD:7 | 28 |
| Water Loss on E | UNIMOD:27 | 23 |
| Hydroxylation on K | UNIMOD:35 | 22 |
| Ammonia loss on N | UNIMOD:385 | 18 |
| N-acetylalanine on A | UNIMOD:1 | 16 |
| Glutarylation on K | UNIMOD:1848 | 15 |
| Sodium on E | UNIMOD:30 | 12 |
| Acetylation on X | UNIMOD:1 | 10 |
| Phosphorylation on S | UNIMOD:21 | 10 |
| Phosphoserine on S | UNIMOD:21 | 10 |
| Acetylation on K | UNIMOD:1 | 8 |
| Dimethylation on K | UNIMOD:36 | 8 |
| Dimethylation on R | UNIMOD:36 | 7 |
| Methylation on R | UNIMOD:34 | 6 |
| Phosphorylation on T | UNIMOD:21 | 6 |
| Phosphothreonine on T | UNIMOD:21 | 6 |
| Formylation on K | UNIMOD:122 | 5 |
| N-acetylmethionine on M | UNIMOD:1 | 5 |
| Omega-N-methylarginine on R | UNIMOD:34 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 4 |
| Magnesium on E | UNIMOD:956 | 4 |
| Methylation on K | UNIMOD:34 | 4 |
| Butyrylation on K | UNIMOD:1289 | 3 |
| Calcium on E | UNIMOD:951 | 3 |
| Carbamyl on X | UNIMOD:5 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| Potassium on E | UNIMOD:530 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| N-acetylthreonine on T | UNIMOD:1 | 2 |
| N6-crotonyllysine on K | — | 2 |
| Succinylation on K | UNIMOD:64 | 2 |
| Sulfonation on Y | UNIMOD:40 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| Calcium on D | UNIMOD:951 | 1 |
| Carbamyl on C | UNIMOD:5 | 1 |
| Carbamyl on M | UNIMOD:5 | 1 |
| Carboxylation on E | UNIMOD:299 | 1 |
| HexNAc on S | UNIMOD:43 | 1 |
| Magnesium on D | UNIMOD:956 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylglycine on G | UNIMOD:1 | 1 |
| N-acetylserine on S | UNIMOD:1 | 1 |
| N6-acetyllysine on K | UNIMOD:1 | 1 |
| Potassium on D | UNIMOD:530 | 1 |
| Sodium on D | UNIMOD:30 | 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
671c8bddecceb3fc, written 2026-10-29T09:21:08+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