Generated summary PXD041660 is a DDA label-free dataset (Mus musculus) with 8 runs, 8 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 122,316 PSMs, 6,419 peptidoforms and 1,224 protein groups, and the repository holds 2,428 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

count_mismatch warning
The bundle holds 122316 where the producer reported 122326 (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.

cysteine_poor warning
0.07% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)

low_core_use warning
10.96 avg cores of 32 allowed (S5)

occupancy_not_stored warning
Of 5092 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 328 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: 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: 4 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
109 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	122,316
Peptidoforms at 1% FDR	6,419
Protein groups at 1% FDR	1,224
PTM sites	2,428
Quantitative values	51,924
PSMs, all (including decoys and sub-threshold)	1,093,910
MS2 identification rate (pxreprise:DEF-ID-RATE)	17.4%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	1.1%

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: 8 / 8
Sample metadata: trusted
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 852cea5e1cd7

Modifications

Search engine's name	UNIMOD	Sites
Oxidation on M	UNIMOD:35	1,316
Hydroxylation on P	UNIMOD:35	250
Carbamidomethyl on C	UNIMOD:4	186
4-hydroxyproline on P	UNIMOD:35	109
Phosphoserine on S	UNIMOD:21	99
Phosphorylation on S	UNIMOD:21	79
Phosphorylation on T	UNIMOD:21	41
Hydroxylation on K	UNIMOD:35	27
N-acetylalanine on A	UNIMOD:1	25
Acetylation on X	UNIMOD:1	23
N-acetylserine on S	UNIMOD:1	23
N6-acetyllysine on K	UNIMOD:1	23
Phosphothreonine on T	UNIMOD:21	21
Methylation on K	UNIMOD:34	18
Asymmetric dimethylarginine on R	UNIMOD:36	14
Omega-N-methylarginine on R	UNIMOD:34	14
5-hydroxylysine on K	UNIMOD:35	11
N-acetylmethionine on M	UNIMOD:1	11
Methylation on R	UNIMOD:34	8
N6,N6-dimethyllysine on K	UNIMOD:36	8
Allysine on K	UNIMOD:352	6
HexNAc on S	UNIMOD:43	6
N6-methyllysine on K	UNIMOD:34	6
Phosphorylation on Y	UNIMOD:21	6
Phosphotyrosine on Y	UNIMOD:21	6
3-hydroxyproline on P	UNIMOD:35	5
Dimethylation on K	UNIMOD:36	5
N6,N6,N6-trimethyllysine on K	UNIMOD:37	5
Dimethylation on R	UNIMOD:36	4
Hydroxyproline on P	UNIMOD:35	4
N-acetylthreonine on T	UNIMOD:1	4
N6-succinyllysine on K	—	4
Tele-methylhistidine on H	UNIMOD:34	4
Acetylation on K	UNIMOD:1	3
Deamidated asparagine on N	UNIMOD:7	3
GG (Ubiquitination Site) on K	UNIMOD:121	3
Malonylation on K	UNIMOD:747	3
N-acetylglycine on G	UNIMOD:1	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
N-acetylvaline on V	UNIMOD:1	2
N6-butyryllysine on K	UNIMOD:1289	2
Pros-methylhistidine on H	UNIMOD:34	2
Crotonylation on K	UNIMOD:1363	1
HexNAc on T	UNIMOD:43	1
N-myristoyl glycine on G	UNIMOD:45	1
N6-biotinyllysine on K	UNIMOD:3	1
Succinylation on K	UNIMOD:64	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: d4c54e0b813669ef, written 2026-10-29T10:15:57+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