Generated summary PXD056433 is a DDA label-free dataset (Rattus norvegicus) with 40 runs, 20 samples and an enrichment step outside the controlled list (recorded as `other`). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 77,681 PSMs, 651 peptidoforms and 240 protein groups, and the repository holds 1,669 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.

Open findings

Recorded against this dataset: 0 errors, 6 warnings and 1 for information

cysteine_poor warning
2.54% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)

low_core_use warning
15.35 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: 77681/529227 = 14.68% of MS2 identified (S3)

occupancy_not_stored warning
Of 6213 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 216 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.

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: 396 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.

What was found

PSMs at 1% FDR	77,681
Peptidoforms at 1% FDR	651
Protein groups at 1% FDR	240
PTM sites	1,669
Quantitative values	43,931
PSMs, all (including decoys and sub-threshold)	286,090
MS2 identification rate (pxreprise:DEF-ID-RATE)	14.7%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	43.3%

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: other
Instrument vendor: not recorded
Runs / samples: 40 / 20
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
Oxidation on M	UNIMOD:35	337
Nethylmaleimide on C	UNIMOD:108	113
Deamidation on Q	UNIMOD:7	90
Deamidation on N	UNIMOD:7	70
Citrullination on R	UNIMOD:7	38
GG (Ubiquitination Site) on K	UNIMOD:121	34
Hydroxylation on P	UNIMOD:35	27
Ammonia loss on N	UNIMOD:385	18
Fe[III] on E	UNIMOD:1870	18
Fe[II] on E	UNIMOD:952	18
Water Loss on E	UNIMOD:27	17
Hydroxylation on K	UNIMOD:35	15
Hydroxylation on N	UNIMOD:35	15
4-hydroxyproline on P	UNIMOD:35	13
Phosphoserine on S	UNIMOD:21	9
Dimethylation on R	UNIMOD:36	7
N-acetylalanine on A	UNIMOD:1	7
N6-acetyllysine on K	UNIMOD:1	6
Acetylation on K	UNIMOD:1	5
Acetylation on X	UNIMOD:1	5
Dimethylation on K	UNIMOD:36	5
Phosphorylation on S	UNIMOD:21	5
Calcium on D	UNIMOD:951	4
N6,N6,N6-trimethyllysine on K	UNIMOD:37	4
N6-methacryllysine on K	—	4
Butyrylation on K	UNIMOD:1289	3
Calcium on E	UNIMOD:951	3
Carboxylation on E	UNIMOD:299	3
Glutarylation on K	UNIMOD:1848	3
Methylation on R	UNIMOD:34	3
N-acetylvaline on V	UNIMOD:1	3
Succinylation on K	UNIMOD:64	3
Symmetric dimethylarginine on R	UNIMOD:36	3
Ammonia loss on C	UNIMOD:385	2
Deamidated asparagine on N	UNIMOD:7	2
Deamidated glutamine on Q	UNIMOD:7	2
HexNAc on T	UNIMOD:43	2
Hydroxybutyrylation on K	—	2
Methylation on K	UNIMOD:34	2
N-acetylmethionine on M	UNIMOD:1	2
N-acetylserine on S	UNIMOD:1	2
N6-methyllysine on K	UNIMOD:34	2
Nitrosylation on Y	UNIMOD:354	2
Omega-N-methylarginine on R	UNIMOD:34	2
Phosphothreonine on T	UNIMOD:21	2
Sodium on E	UNIMOD:30	2
3'-nitrotyrosine on Y	—	1
4-carboxyglutamate on E	UNIMOD:299	1
Asymmetric dimethylarginine on R	UNIMOD:36	1
Fe[III] on D	UNIMOD:1870	1
Fe[II] on D	UNIMOD:952	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglycine on G	UNIMOD:1	1
N6-succinyllysine on K	—	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
Sodium on D	UNIMOD:30	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: e9eee20a0f8fd141, written 2026-10-29T09:30:16+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