Generated summary PXD058775 is a DDA label-free dataset (Mus musculus) with 18 runs, 18 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 1,859 PSMs, 226 peptidoforms and 153 protein groups, and the repository holds 128 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

calibration_failed warning
GPTMD/search ran on uncalibrated spectra (S7)

contaminant_label_unresolved warning
3 protein(s) share a PSM row with proteins of another kind, and the searched databases could not say which they are (not on disk, or in both a target and the contaminant database under TCAmbiguity unknown). Each was given its row's label, contaminant over target, so `is_contaminant` may over-state for them: P05784, Q99PS0, Q9DCV7.

high_contamination warning
13.96% of protein intensity in the worst file, 10.33% median across 18 files (DEF-QC-9 v3.5)

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: 1859/1164723 = 0.16% of MS2 identified (S3)

no_design_file warning
No experimental design file, so quantification treated every raw file as its own condition. Between-group comparisons are not available for this dataset. Producer's note: FlashLFQ treated each file as its own biorep under one blank condition; no normalization; not usable for condition comparisons (owner: QuantProject projection)

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.

no_output_sdrf info
The search did not write an SDRF back out, so sample metadata comes from the deposited SDRF only. Producer's note: no reanalysis SDRF written (WriteSdrf is MetaMorpheus #2816, unreleased)

What was found

PSMs at 1% FDR	1,859
Peptidoforms at 1% FDR	226
Protein groups at 1% FDR	153
PTM sites	128
Quantitative values	6,229
PSMs, all (including decoys and sub-threshold)	18,011
MS2 identification rate (pxreprise:DEF-ID-RATE)	0.2%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	18.3%

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: not recorded
Runs / samples: 18 / 18
Sample metadata: absent
Search engine: MetaMorpheus 1.1.11
Protein database: uniprotkb_proteome_UP000000589_AND_revi_2026-09-22_agingPTM-v1.xml
Pipeline commit: 6a36ecb6037c

Modifications

Search engine's name	UNIMOD	Sites
Oxidation on M	UNIMOD:35	72
Carbamidomethyl on C	UNIMOD:4	20
N6-acetyllysine on K	UNIMOD:1	10
N-acetylalanine on A	UNIMOD:1	3
4-hydroxyproline on P	UNIMOD:35	2
Deamidated asparagine on N	UNIMOD:7	2
N6,N6,N6-trimethyllysine on K	UNIMOD:37	2
N-acetylglutamate on E	UNIMOD:1	1
N-acetylmethionine on M	UNIMOD:1	1
N-acetylserine on S	UNIMOD:1	1
N-acetylthreonine on T	UNIMOD:1	1
N6,N6-dimethyllysine on K	UNIMOD:36	1
Phosphothreonine 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: 0e7f1a278d64e536, written 2026-10-29T09:53:09+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