Generated summary PXD022363 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 56,170 PSMs, 9,054 peptidoforms and 1,565 protein groups, and the repository holds 4,726 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

high_contamination warning
10.12% of protein intensity in the worst file, 3.90% median across 12 files (DEF-QC-9 v3.5)

low_core_use warning
8.5 avg cores of 32 allowed (S5)

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.

occupancy_not_stored warning
Of 2454 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 695 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).

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: 64 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
49 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	56,170
Peptidoforms at 1% FDR	9,054
Protein groups at 1% FDR	1,565
PTM sites	4,726
Quantitative values	108,410
PSMs, all (including decoys and sub-threshold)	388,424
MS2 identification rate (pxreprise:DEF-ID-RATE)	28.5%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	3.7%

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: not recorded
Runs / samples: 12 / 12
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: aae950b1861c

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	2,671
Oxidation on M	UNIMOD:35	1,442
Hydroxylation on P	UNIMOD:35	162
Phosphoserine on S	UNIMOD:21	65
N-acetylalanine on A	UNIMOD:1	39
4-hydroxyproline on P	UNIMOD:35	34
N-acetylserine on S	UNIMOD:1	28
Acetylation on X	UNIMOD:1	24
Hydroxylation on K	UNIMOD:35	19
N6-acetyllysine on K	UNIMOD:1	16
N-acetylmethionine on M	UNIMOD:1	14
HexNAc on S	UNIMOD:43	11
Omega-N-methylarginine on R	UNIMOD:34	9
Phosphorylation on S	UNIMOD:21	8
HexNAc on T	UNIMOD:43	7
N-acetylthreonine on T	UNIMOD:1	7
5-hydroxylysine on K	UNIMOD:35	6
Phosphothreonine on T	UNIMOD:21	6
Deamidated asparagine on N	UNIMOD:7	5
N6-succinyllysine on K	—	5
Tele-methylhistidine on H	UNIMOD:34	5
Asymmetric dimethylarginine on R	UNIMOD:36	4
Methylation on K	UNIMOD:34	4
Methylation on R	UNIMOD:34	4
N6,N6,N6-trimethyllysine on K	UNIMOD:37	4
N6,N6-dimethyllysine on K	UNIMOD:36	4
N-acetylglycine on G	UNIMOD:1	3
Phosphorylation on T	UNIMOD:21	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Acetylation on K	UNIMOD:1	2
GG (Ubiquitination Site) on K	UNIMOD:121	2
N6-methyllysine on K	UNIMOD:34	2
3-hydroxyproline on P	UNIMOD:35	1
Allysine on K	UNIMOD:352	1
Dimethylated arginine on R	UNIMOD:36	1
Dimethylation on K	UNIMOD:36	1
Glutarylation on K	UNIMOD:1848	1
Hydroxyproline on P	UNIMOD:35	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-malonyllysine on K	—	1
S-nitrosocysteine on C	UNIMOD:275	1
Succinylation on K	UNIMOD:64	1
Tele-8alpha-FAD histidine on H	UNIMOD:50	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: 9798c839fcd2f786, written 2026-10-29T10:02:51+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