Generated summary PXD043644 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 88,987 PSMs, 1,558 peptidoforms and 399 protein groups, and the repository holds 2,268 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

high_contamination warning
63.58% of protein intensity in the worst file, 33.01% median across 12 files (DEF-QC-9 v3.5)

low_core_use warning
10.9 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: 88987/1487500 = 5.98% 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 1501 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 31 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).

occupancy_decoy_groups info
173 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	88,987
Peptidoforms at 1% FDR	1,558
Protein groups at 1% FDR	399
PTM sites	2,268
Quantitative values	51,228
PSMs, all (including decoys and sub-threshold)	2,416,545
MS2 identification rate (pxreprise:DEF-ID-RATE)	6.0%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	51.7%

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: 12 / 12
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 0095bcefc3f5

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	865
Oxidation on M	UNIMOD:35	652
Hydroxylation on P	UNIMOD:35	79
Phosphorylation on S	UNIMOD:21	71
Phosphoserine on S	UNIMOD:21	68
Phosphorylation on T	UNIMOD:21	39
N6-succinyllysine on K	—	25
Omega-N-methylarginine on R	UNIMOD:34	19
Hydroxylation on K	UNIMOD:35	18
4-hydroxyproline on P	UNIMOD:35	15
N6-acetyllysine on K	UNIMOD:1	12
N-acetylalanine on A	UNIMOD:1	11
HexNAc on S	UNIMOD:43	9
HexNAc on T	UNIMOD:43	9
Asymmetric dimethylarginine on R	UNIMOD:36	8
Malonylation on K	UNIMOD:747	8
Acetylation on X	UNIMOD:1	7
Methylation on K	UNIMOD:34	7
N-acetylserine on S	UNIMOD:1	7
Phosphorylation on Y	UNIMOD:21	7
Methylation on R	UNIMOD:34	6
Dimethylation on K	UNIMOD:36	5
Phosphothreonine on T	UNIMOD:21	5
N-acetylmethionine on M	UNIMOD:1	4
Dimethylation on R	UNIMOD:36	3
GG (Ubiquitination Site) on K	UNIMOD:121	3
Succinylation on K	UNIMOD:64	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
5-hydroxylysine on K	UNIMOD:35	2
Acetylation on K	UNIMOD:1	2
Crotonylation on K	UNIMOD:1363	2
N6,N6-dimethyllysine on K	UNIMOD:36	2
Phosphotyrosine on Y	UNIMOD:21	2
3-hydroxyproline on P	UNIMOD:35	1
Allysine on K	UNIMOD:352	1
Butyrylation on K	UNIMOD:1289	1
Citrulline on R	UNIMOD:7	1
Deamidated asparagine on N	UNIMOD:7	1
Deamidated glutamine on Q	UNIMOD:7	1
Dimethylated arginine on R	UNIMOD:36	1
Glutarylation on K	UNIMOD:1848	1
Hydroxyproline on P	UNIMOD:35	1
N-acetylglutamate on E	UNIMOD:1	1
N-acetylglycine on G	UNIMOD:1	1
N5-methylglutamine on Q	UNIMOD:34	1
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	1
N6-(beta-hydroxybutyryl)lysine on K	UNIMOD:1849	1
N6-butyryllysine on K	UNIMOD:1289	1
N6-methyllysine on K	UNIMOD:34	1
Sulfotyrosine on Y	UNIMOD:40	1
Tele-methylhistidine on H	UNIMOD:34	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: 74efd58d3f1d36aa, written 2026-10-29T11:59:49+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