Generated summary PXD059520 is a DDA label-free dataset (Rattus norvegicus) with 21 runs, 21 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 162,200 PSMs, 8,846 peptidoforms and 1,681 protein groups, and the repository holds 5,807 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

count_mismatch warning
The bundle holds 162200 where the producer reported 162242 (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.

low_core_use warning
8.42 avg cores of 32 allowed (S5)

no_sdrf warning
No SDRF was found for this dataset, so each run was given a synthetic sample of its own. There is no sample metadata: treat every sample as unannotated.

occupancy_not_stored warning
Of 6853 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2950 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).

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: 922 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
44 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	162,200
Peptidoforms at 1% FDR	8,846
Protein groups at 1% FDR	1,681
PTM sites	5,807
Quantitative values	215,484
PSMs, all (including decoys and sub-threshold)	907,284
MS2 identification rate (pxreprise:DEF-ID-RATE)	40.5%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	0.8%

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: none
Instrument vendor: not recorded
Runs / samples: 21 / 21
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000002494_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 5aec9eb024d8

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	3,830
Oxidation on M	UNIMOD:35	1,317
Phosphoserine on S	UNIMOD:21	142
N-acetylalanine on A	UNIMOD:1	78
N-acetylserine on S	UNIMOD:1	41
Hydroxylation on P	UNIMOD:35	40
Phosphothreonine on T	UNIMOD:21	33
N-acetylmethionine on M	UNIMOD:1	29
Deamidated asparagine on N	UNIMOD:7	24
N6-acetyllysine on K	UNIMOD:1	20
Acetylation on X	UNIMOD:1	18
4-hydroxyproline on P	UNIMOD:35	17
Methylation on K	UNIMOD:34	14
Omega-N-methylarginine on R	UNIMOD:34	13
Asymmetric dimethylarginine on R	UNIMOD:36	9
N6,N6,N6-trimethyllysine on K	UNIMOD:37	8
N-acetylthreonine on T	UNIMOD:1	7
3'-nitrotyrosine on Y	—	5
5-hydroxylysine on K	UNIMOD:35	5
HexNAc on T	UNIMOD:43	5
N-myristoyl glycine on G	UNIMOD:45	5
N6,N6-dimethyllysine on K	UNIMOD:36	5
N6-succinyllysine on K	—	5
Cysteine persulfide on C	UNIMOD:421	4
Hydroxylation on K	UNIMOD:35	4
N-acetylvaline on V	UNIMOD:1	4
Phosphotyrosine on Y	UNIMOD:21	4
S-(2-succinyl)cysteine on C	UNIMOD:957	4
Tele-methylhistidine on H	UNIMOD:34	4
Trimethylation on K	UNIMOD:37	4
Acetylation on K	UNIMOD:1	3
Dimethylated arginine on R	UNIMOD:36	3
HexNAc on S	UNIMOD:43	3
N-acetylglycine on G	UNIMOD:1	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Deamidated glutamine on Q	UNIMOD:7	2
Dimethylation on R	UNIMOD:36	2
Glutarylation on K	UNIMOD:1848	2
N-acetylcysteine on C	UNIMOD:1	2
N6-methyllysine on K	UNIMOD:34	2
S-geranylgeranyl cysteine on C	UNIMOD:48	2
Citrulline on R	UNIMOD:7	1
Crotonylation on K	UNIMOD:1363	1
Cysteine sulfinic acid (-SO2H) on C	UNIMOD:425	1
Dimethylation on K	UNIMOD:36	1
Hydroxybutyrylation on K	—	1
Methylation on R	UNIMOD:34	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	1
Phosphorylation on S	UNIMOD:21	1
Phosphorylation on T	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: 90e9324979e1e90b, written 2026-10-29T11:47:04+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