Generated summary PXD047289 is a DDA label-free dataset (Rattus norvegicus) with 22 runs, 11 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 37,693 PSMs, 3,402 peptidoforms and 1,035 protein groups, and the repository holds 2,493 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

count_mismatch warning
The bundle holds 37693 where the producer reported 37695 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.

cysteine_poor warning
1.14% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)

low_core_use warning
14.18 avg cores of 32 allowed (S5)

occupancy_not_stored warning
Of 7888 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 319 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: 241 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
22 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	37,693
Peptidoforms at 1% FDR	3,402
Protein groups at 1% FDR	1,035
PTM sites	2,493
Quantitative values	62,983
PSMs, all (including decoys and sub-threshold)	161,185
MS2 identification rate (pxreprise:DEF-ID-RATE)	15.4%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	33.8%

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: 22 / 11
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	1,021
Deamidation on N	UNIMOD:7	115
Hydroxylation on P	UNIMOD:35	92
Nethylmaleimide on C	UNIMOD:108	85
Deamidation on Q	UNIMOD:7	59
4-hydroxyproline on P	UNIMOD:35	45
Hydroxylation on N	UNIMOD:35	30
Phosphoserine on S	UNIMOD:21	23
Acetylation on X	UNIMOD:1	17
Phosphorylation on S	UNIMOD:21	17
N-acetylalanine on A	UNIMOD:1	16
Ammonia loss on N	UNIMOD:385	12
Dimethylation on R	UNIMOD:36	9
Hydroxylation on K	UNIMOD:35	9
N-acetylserine on S	UNIMOD:1	9
Phosphothreonine on T	UNIMOD:21	9
Dimethylation on K	UNIMOD:36	8
Water Loss on E	UNIMOD:27	8
N-acetylmethionine on M	UNIMOD:1	7
Citrullination on R	UNIMOD:7	6
Formylation on K	UNIMOD:122	6
GG (Ubiquitination Site) on K	UNIMOD:121	5
Omega-N-methylarginine on R	UNIMOD:34	5
Phosphorylation on T	UNIMOD:21	5
Acetylation on K	UNIMOD:1	4
Deamidated asparagine on N	UNIMOD:7	4
Methylation on K	UNIMOD:34	3
N-acetylthreonine on T	UNIMOD:1	3
Symmetric dimethylarginine on R	UNIMOD:36	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Carbamyl on X	UNIMOD:5	2
Crotonylation on K	UNIMOD:1363	2
Deamidated glutamine on Q	UNIMOD:7	2
Fe[III] on E	UNIMOD:1870	2
N-acetylvaline on V	UNIMOD:1	2
N6-methyllysine on K	UNIMOD:34	2
Nitrosylation on C	UNIMOD:275	2
Tele-methylhistidine on H	UNIMOD:34	2
3-hydroxyproline on P	UNIMOD:35	1
5-hydroxylysine on K	UNIMOD:35	1
Ammonia loss on C	UNIMOD:385	1
Asymmetric dimethylarginine on R	UNIMOD:36	1
Butyrylation on K	UNIMOD:1289	1
Calcium on D	UNIMOD:951	1
Calcium on E	UNIMOD:951	1
Carbamyl on K	UNIMOD:5	1
Carbamyl on M	UNIMOD:5	1
Fe[III] on D	UNIMOD:1870	1
HexNAc on T	UNIMOD:43	1
Hydroxybutyrylation on K	—	1
N-acetylglycine on G	UNIMOD:1	1
N6-acetyllysine on K	UNIMOD:1	1
Sodium on D	UNIMOD:30	1
Sulfonation on Y	UNIMOD:40	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: ee6cfbd52cb09a8d, written 2026-10-29T09:43:48+00:00 by ingester 1.4.0
Reconciliation: failed: psms_target_1pct (the bundle disagrees with the producer's own count here)
Licence: CC-BY-4.0
Credit: NCEMS Aging Proteome Working Group