Generated summary PXD036557 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 26,582 PSMs, 5,541 peptidoforms and 1,652 protein groups, and the repository holds 2,091 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 2 for information

high_contamination warning
18.92% of protein intensity in the worst file, 5.50% median across 18 files (DEF-QC-9 v2)

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: 26582/266402 = 9.98% 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)

sdrf_skeleton warning
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.

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: 30 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.

upstream_provenance_changed warning
The search recorded its upstream 'db_prepare' provenance (db/provenance.json) with sha256 6c40902506a8bd4a99fe884bae6d95be46f8a1647d50570879ddcd3b3a79de59, and the file there now has 812ce696ba3f0ee2a1f79241b5e16e9267d6199f7598af77391178b825658963: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the db_prepare stage is gone unless the producer archived it.

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)

occupancy_decoy_groups info
9 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	26,582
Peptidoforms at 1% FDR	5,541
Protein groups at 1% FDR	1,652
PTM sites	2,091
Quantitative values	78,411
PSMs, all (including decoys and sub-threshold)	42,958
MS2 identification rate (aging:DEF-ID-RATE)	10.0%
Contaminant share of PSMs (aging:DEF-CONTAM-PSM)	3.9%

How it was measured

Organism searched: Homo sapiens (the protein database's organism, not a statement about the samples)
Acquisition: DDA
Quantification: label_free
Labelling: none
Enrichment: none
Instrument vendor: Thermo
Runs / samples: 18 / 18
Sample metadata: trusted
Search engine: MetaMorpheus 1.1.11
Protein database: uniprotkb_proteome_UP000005640_AND_revi_2026_09_18.xml
Pipeline commit: 4ea7670404cb572729c2ade4b19e625b2ebc4241

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	1,308
Deamidation on N	UNIMOD:7	187
Oxidation on M	UNIMOD:35	114
Deamidation on Q	UNIMOD:7	41
N-acetylalanine on A	UNIMOD:1	39
N6-acetyllysine on K	UNIMOD:1	39
Hydroxylation on P	UNIMOD:35	38
Hydroxylation on K	UNIMOD:35	25
Calcium on D	UNIMOD:951	21
4-hydroxyproline on P	UNIMOD:35	20
N-acetylmethionine on M	UNIMOD:1	14
Ammonia loss on N	UNIMOD:385	13
Ammonia loss on C	UNIMOD:385	12
Hydroxylation on N	UNIMOD:35	11
N-acetylserine on S	UNIMOD:1	11
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	10
Asymmetric dimethylarginine on R	UNIMOD:36	8
N6,N6,N6-trimethyllysine on K	UNIMOD:37	7
N-acetylthreonine on T	UNIMOD:1	6
N6-methyllysine on K	UNIMOD:34	6
Phosphoserine on S	UNIMOD:21	6
Deamidated asparagine on N	UNIMOD:7	5
Citrullination on R	UNIMOD:7	3
N6,N6-dimethyllysine on K	UNIMOD:36	3
Tele-methylhistidine on H	UNIMOD:34	3
Water Loss on E	UNIMOD:27	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Calcium on E	UNIMOD:951	2
Hydroxyproline on P	UNIMOD:35	2
Methylation on R	UNIMOD:34	2
Omega-N-methylarginine on R	UNIMOD:34	2
5-hydroxylysine on K	UNIMOD:35	1
Methylation on K	UNIMOD:34	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N-acetylglycine on G	UNIMOD:1	1
N-acetylvaline on V	UNIMOD:1	1
N-myristoyl glycine on G	UNIMOD:45	1
N6-succinyllysine on K	—	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: 0955c951b61e80ba, written 2026-10-29T09:52:18+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