Generated summary PXD058248 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 43,066 PSMs, 629 peptidoforms and 239 protein groups, and the repository holds 1,955 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.

Open findings

Recorded against this dataset: 0 errors, 4 warnings and 1 for information

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: 43066/600088 = 7.18% of MS2 identified (S3)

occupancy_not_stored warning
Of 8769 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 260 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: 57 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
177 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	43,066
Peptidoforms at 1% FDR	629
Protein groups at 1% FDR	239
PTM sites	1,955
Quantitative values	42,510
PSMs, all (including decoys and sub-threshold)	455,420
MS2 identification rate (pxreprise:DEF-ID-RATE)	7.2%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	62.3%

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: 38 / 19
Sample metadata: trusted
Search engine: MetaMorpheus 1.1.12
Protein database: UP000002494_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 8d67a57e54cf

Modifications

Search engine's name	UNIMOD	Sites
Oxidation on M	UNIMOD:35	394
Nethylmaleimide on C	UNIMOD:108	240
Hydroxylation on P	UNIMOD:35	86
Deamidation on N	UNIMOD:7	79
Deamidation on Q	UNIMOD:7	68
Hydroxylation on N	UNIMOD:35	63
GG (Ubiquitination Site) on K	UNIMOD:121	38
Citrullination on R	UNIMOD:7	31
Glutarylation on K	UNIMOD:1848	23
Hydroxylation on K	UNIMOD:35	20
Sodium on D	UNIMOD:30	17
Magnesium on D	UNIMOD:956	16
Fe[II] on E	UNIMOD:952	14
Phosphoserine on S	UNIMOD:21	13
Sodium on E	UNIMOD:30	13
Ammonia loss on N	UNIMOD:385	12
Phosphorylation on S	UNIMOD:21	12
N-acetylalanine on A	UNIMOD:1	11
Dimethylation on K	UNIMOD:36	9
Magnesium on E	UNIMOD:956	9
Calcium on E	UNIMOD:951	8
Fe[III] on E	UNIMOD:1870	8
Phosphorylation on T	UNIMOD:21	8
Acetylation on K	UNIMOD:1	6
Deamidated asparagine on N	UNIMOD:7	6
Methylation on K	UNIMOD:34	6
Dimethylation on R	UNIMOD:36	5
Formylation on K	UNIMOD:122	5
HexNAc on T	UNIMOD:43	5
Malonylation on K	UNIMOD:747	5
N6-acetyllysine on K	UNIMOD:1	5
Calcium on D	UNIMOD:951	4
HexNAc on S	UNIMOD:43	4
Hydroxybutyrylation on K	—	4
Methylation on R	UNIMOD:34	4
Phosphothreonine on T	UNIMOD:21	4
Potassium on D	UNIMOD:530	4
Potassium on E	UNIMOD:530	4
Acetylation on X	UNIMOD:1	3
Carboxylation on E	UNIMOD:299	3
Fe[III] on D	UNIMOD:1870	3
Fe[II] on D	UNIMOD:952	3
N-acetylmethionine on M	UNIMOD:1	3
N-acetylvaline on V	UNIMOD:1	3
Pyridoxal phosphate on K	UNIMOD:46	3
Carboxylation on D	UNIMOD:299	2
Crotonylation on K	UNIMOD:1363	2
Deamidated glutamine on Q	UNIMOD:7	2
N6,N6,N6-trimethyllysine on K	UNIMOD:37	2
N6-succinyllysine on K	—	2
Nitrosylation on C	UNIMOD:275	2
Omega-N-methylarginine on R	UNIMOD:34	2
Phosphorylation on Y	UNIMOD:21	2
Sulfonation on Y	UNIMOD:40	2
Tele-methylhistidine on H	UNIMOD:34	2
3'-nitrotyrosine on Y	—	1
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	1
Butyrylation on K	UNIMOD:1289	1
Carboxylation on K	UNIMOD:299	1
Cysteine persulfide on C	UNIMOD:421	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,N6-dimethyllysine on K	UNIMOD:36	1
Phosphotyrosine on Y	UNIMOD:21	1
S-nitrosocysteine on C	UNIMOD:275	1
Succinylation on K	UNIMOD:64	1
Trimethylation on K	UNIMOD:37	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: 0d7759b6e42795cd, written 2026-10-29T09:07:32+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