Generated summary PXD055228 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 2,687 PSMs, 331 peptidoforms and 130 protein groups, and the repository holds 267 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

high_contamination warning
61.90% of protein intensity in the worst file, 33.87% median across 15 files (DEF-QC-9 v3.5)

low_core_use warning
11.62 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: 2687/144760 = 1.86% of MS2 identified (S3)

mbr_kept_exceeds_msms warning
kept MBR 4689 > MSMS 4176 (DEF-MBR-KEPT v1)

occupancy_not_stored warning
Of 980 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 142 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_partial warning
The SDRF was used only for the runs it names that were searched: it names 5 file(s) the search did not use, whose rows were not used: Sample2a_02, Sample4a_01, Sample4a_02, Sample5a_01, Sample5b_01. sdrf_status is `partial`.

sdrf_uncoded warning
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: cell type: mesenchymal cell. Match on it as text; it has not been mapped to a term.

occupancy_decoy_groups info
6 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	2,687
Peptidoforms at 1% FDR	331
Protein groups at 1% FDR	130
PTM sites	267
Quantitative values	13,821
PSMs, all (including decoys and sub-threshold)	12,543
MS2 identification rate (pxreprise:DEF-ID-RATE)	1.9%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	54.8%

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: immunoprecipitation
Instrument vendor: Thermo
Runs / samples: 15 / 15
Sample metadata: partial
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
Oxidation on M	UNIMOD:35	50
Carbamidomethyl on C	UNIMOD:4	28
Deamidation on N	UNIMOD:7	8
Hydroxylation on P	UNIMOD:35	7
N-acetylalanine on A	UNIMOD:1	7
Hydroxylation on N	UNIMOD:35	4
N6,N6,N6-trimethyllysine on K	UNIMOD:37	4
Deamidation on Q	UNIMOD:7	3
Acetylation on K	UNIMOD:1	2
Ammonia loss on N	UNIMOD:385	2
Citrullination on R	UNIMOD:7	2
Glu to PyroGlu on Q	UNIMOD:28	2
Tele-methylhistidine on H	UNIMOD:34	2
Acetylation on X	UNIMOD:1	1
Hydroxylation on K	UNIMOD:35	1
Methylation on R	UNIMOD:34	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylcysteine on C	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N-acetylmethionine on M	UNIMOD:1	1
N-acetylserine on S	UNIMOD:1	1
N-acetylvaline on V	UNIMOD:1	1
N6,N6-dimethyllysine on K	UNIMOD:36	1
Phosphorylation 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: 2d81ffbb155046e8, written 2026-10-29T09:53:24+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