Generated summary PXD047292 is a DDA label-free dataset (Rattus norvegicus) with 36 runs, 18 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 10,059 PSMs, 698 peptidoforms and 240 protein groups, and the repository holds 1,568 PTM sites for it. 5 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, 5 warnings and 1 for information

cysteine_poor warning
0.70% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)

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: 10059/560252 = 1.80% of MS2 identified (S3)

occupancy_not_stored warning
Of 9591 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 243 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: 116 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
3 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	10,059
Peptidoforms at 1% FDR	698
Protein groups at 1% FDR	240
PTM sites	1,568
Quantitative values	30,420
PSMs, all (including decoys and sub-threshold)	188,526
MS2 identification rate (pxreprise:DEF-ID-RATE)	1.8%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	68.1%

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 / 18
Sample metadata: trusted
Search engine: MetaMorpheus 1.1.12
Protein database: UP000002494_all_genecentric_2026_03_agingPTM-v4.xml
Pipeline commit: 9df4ce025f23

Modifications

Search engine's name	UNIMOD	Sites
Oxidation on M	UNIMOD:35	229
Formylation on K	UNIMOD:122	45
Hydroxylation on P	UNIMOD:35	42
GG (Ubiquitination Site) on K	UNIMOD:121	34
Deamidation on N	UNIMOD:7	22
Deamidation on Q	UNIMOD:7	21
4-hydroxyproline on P	UNIMOD:35	19
Citrullination on R	UNIMOD:7	18
Ammonia loss on N	UNIMOD:385	17
Nethylmaleimide on C	UNIMOD:108	17
Acetylation on K	UNIMOD:1	14
Hydroxylation on N	UNIMOD:35	12
Acetylation on X	UNIMOD:1	11
N-acetylalanine on A	UNIMOD:1	9
Methylation on K	UNIMOD:34	7
Hydroxylation on K	UNIMOD:35	5
Dimethylation on R	UNIMOD:36	4
Methylation on R	UNIMOD:34	4
N-acetylmethionine on M	UNIMOD:1	4
Carbamyl on X	UNIMOD:5	3
Crotonylation on K	UNIMOD:1363	3
Deamidated asparagine on N	UNIMOD:7	3
Phosphothreonine on T	UNIMOD:21	3
Sulfonation on Y	UNIMOD:40	3
Symmetric dimethylarginine on R	UNIMOD:36	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Deamidated glutamine on Q	UNIMOD:7	2
Dimethylation on K	UNIMOD:36	2
Hydroxybutyrylation on K	—	2
N-acetylvaline on V	UNIMOD:1	2
Omega-N-methylarginine on R	UNIMOD:34	2
Phosphorylation on S	UNIMOD:21	2
Tele-methylhistidine on H	UNIMOD:34	2
Water Loss on E	UNIMOD:27	2
5-hydroxylysine on K	UNIMOD:35	1
Butyrylation on K	UNIMOD:1289	1
Carbamyl on K	UNIMOD:5	1
Carboxylation on E	UNIMOD:299	1
HexNAc on S	UNIMOD:43	1
HexNAc on T	UNIMOD:43	1
Magnesium on D	UNIMOD:956	1
N-acetylglycine on G	UNIMOD:1	1
N-acetylserine on S	UNIMOD:1	1
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	1
N6-acetyllysine on K	UNIMOD:1	1
N6-glutaryllysine on K	—	1
N6-isonicotinyllysine on K	UNIMOD:697	1
Phosphorylation on T	UNIMOD:21	1
Phosphoserine on S	UNIMOD:21	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: 233f8e542c1ba555, written 2026-10-29T09:42:22+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