Generated summary PXD018545 is a DDA label-free dataset (Mus musculus) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 316,110 PSMs, 7,742 peptidoforms and 1,037 protein groups, and the repository holds 7,211 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

count_mismatch warning
The bundle holds 316110 where the producer reported 316114 (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.

low_core_use warning
9.88 avg cores of 32 allowed (S5)

occupancy_not_stored warning
Of 5969 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1057 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_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: disease: normal; organism part: heart. Match on it as text; it has not been mapped to a term.

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: 45 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
274 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	316,110
Peptidoforms at 1% FDR	7,742
Protein groups at 1% FDR	1,037
PTM sites	7,211
Quantitative values	198,800
PSMs, all (including decoys and sub-threshold)	3,098,172
MS2 identification rate (pxreprise:DEF-ID-RATE)	16.7%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	1.2%

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: Thermo
Runs / samples: 18 / 18
Sample metadata: trusted
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 6ea39b9e1b3a

Modifications

Search engine's name	UNIMOD	Sites
Oxidation on M	UNIMOD:35	3,408
Carbamidomethyl on C	UNIMOD:4	2,801
Hydroxylation on P	UNIMOD:35	172
Phosphoserine on S	UNIMOD:21	166
N6-acetyllysine on K	UNIMOD:1	100
N6-succinyllysine on K	—	44
N-acetylalanine on A	UNIMOD:1	42
Hydroxylation on K	UNIMOD:35	38
4-hydroxyproline on P	UNIMOD:35	37
Acetylation on X	UNIMOD:1	26
Phosphothreonine on T	UNIMOD:21	23
Omega-N-methylarginine on R	UNIMOD:34	22
HexNAc on T	UNIMOD:43	20
HexNAc on S	UNIMOD:43	18
Acetylation on K	UNIMOD:1	16
N-acetylmethionine on M	UNIMOD:1	15
Methylation on R	UNIMOD:34	14
N-acetylserine on S	UNIMOD:1	13
Methylation on K	UNIMOD:34	11
5-hydroxylysine on K	UNIMOD:35	6
Asymmetric dimethylarginine on R	UNIMOD:36	6
Dimethylation on K	UNIMOD:36	6
Trimethylation on K	UNIMOD:37	6
Allysine on K	UNIMOD:352	5
GG (Ubiquitination Site) on K	UNIMOD:121	4
Glutarylation on K	UNIMOD:1848	4
N6-methyllysine on K	UNIMOD:34	4
Phosphorylation on S	UNIMOD:21	4
Succinylation on K	UNIMOD:64	4
Tele-methylhistidine on H	UNIMOD:34	4
3-hydroxyproline on P	UNIMOD:35	3
Butyrylation on K	UNIMOD:1289	3
Crotonylation on K	UNIMOD:1363	3
Dimethylation on R	UNIMOD:36	3
N-acetylglycine on G	UNIMOD:1	3
N-acetylthreonine on T	UNIMOD:1	3
N-myristoyl glycine on G	UNIMOD:45	3
N6,N6,N6-trimethyllysine on K	UNIMOD:37	3
Phosphorylation on T	UNIMOD:21	3
N6-methacryllysine on K	—	2
Cysteine sulfinic acid (-SO2H) on C	UNIMOD:425	1
Deamidated asparagine on N	UNIMOD:7	1
Deamidated glutamine on Q	UNIMOD:7	1
Hydroxybutyrylation on K	—	1
Malonylation on K	UNIMOD:747	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylcysteine on C	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N-acetylvaline on V	UNIMOD:1	1
N6,N6-dimethyllysine on K	UNIMOD:36	1
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	1
N6-glutaryllysine on K	—	1
N6-lipoyllysine on K	UNIMOD:42	1
Phosphotyrosine on Y	UNIMOD:21	1
Pros-methylhistidine on H	UNIMOD:34	1
Symmetric dimethylarginine on R	UNIMOD:36	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: a68620f1dcff66c8, written 2026-10-29T10:07:48+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