Generated summary PXD052631 is a DDA label-free dataset (Mus musculus) with 22 runs, 22 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 41,561 PSMs, 3,855 peptidoforms and 1,003 protein groups, and the repository holds 3,303 PTM sites for it. 7 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, 7 warnings and 1 for information

count_mismatch warning
The bundle holds 41561 where the producer reported 41562 (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.

high_contamination warning
57.82% of protein intensity in the worst file, 40.72% median across 22 files (DEF-QC-9 v3.5)

low_core_use warning
9.54 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: 41562/361002 = 11.51% of MS2 identified (S3)

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 5824 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2828 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: 120 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
61 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	41,561
Peptidoforms at 1% FDR	3,855
Protein groups at 1% FDR	1,003
PTM sites	3,303
Quantitative values	89,300
PSMs, all (including decoys and sub-threshold)	508,198
MS2 identification rate (pxreprise:DEF-ID-RATE)	11.5%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	32.4%

How it was measured

Organism searched: Mus musculus (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: 22 / 22
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 9df4ce025f23

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	1,178
Oxidation on M	UNIMOD:35	964
N-acetylalanine on A	UNIMOD:1	136
Phosphoserine on S	UNIMOD:21	72
Hydroxylation on P	UNIMOD:35	58
N-acetylserine on S	UNIMOD:1	57
N-acetylmethionine on M	UNIMOD:1	46
Phosphorylation on S	UNIMOD:21	41
Acetylation on X	UNIMOD:1	35
N6-acetyllysine on K	UNIMOD:1	33
Phosphorylation on T	UNIMOD:21	28
N6-methyllysine on K	UNIMOD:34	19
N6,N6-dimethyllysine on K	UNIMOD:36	17
Deamidated asparagine on N	UNIMOD:7	16
Methylation on K	UNIMOD:34	16
4-hydroxyproline on P	UNIMOD:35	12
Hydroxylation on K	UNIMOD:35	8
N-acetylthreonine on T	UNIMOD:1	8
Dimethylation on K	UNIMOD:36	7
Phosphothreonine on T	UNIMOD:21	7
Asymmetric dimethylarginine on R	UNIMOD:36	6
N6,N6,N6-trimethyllysine on K	UNIMOD:37	6
Acetylation on K	UNIMOD:1	5
N-acetylproline on P	UNIMOD:1	5
Phosphorylation on Y	UNIMOD:21	5
N-acetylglycine on G	UNIMOD:1	3
N-acetylvaline on V	UNIMOD:1	3
N5-methylglutamine on Q	UNIMOD:34	3
HexNAc on S	UNIMOD:43	2
Hydroxybutyrylation on K	—	2
Malonylation on K	UNIMOD:747	2
Methylation on R	UNIMOD:34	2
N6-succinyllysine on K	—	2
Phosphotyrosine on Y	UNIMOD:21	2
Tele-methylhistidine on H	UNIMOD:34	2
3-hydroxyproline on P	UNIMOD:35	1
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	1
Cysteine persulfide on C	UNIMOD:421	1
GG (Ubiquitination Site) on K	UNIMOD:121	1
Glutarylation on K	UNIMOD:1848	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylcysteine on C	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N-myristoyl glycine on G	UNIMOD:45	1
Pros-methylhistidine on H	UNIMOD:34	1
Succinylation on K	UNIMOD:64	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: f2e398f48a25d809, written 2026-10-29T11:19:34+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