Generated summary PXD033430 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and enrichment: acetyl. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 29,476 PSMs, 3,084 peptidoforms and 1,318 protein groups, and the repository holds 2,817 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

low_core_use warning
8.48 avg cores of 32 allowed (S5)

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: 29476/232385 = 12.68% of MS2 identified (S3)

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 5281 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 473 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: 127 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
14 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	29,476
Peptidoforms at 1% FDR	3,084
Protein groups at 1% FDR	1,318
PTM sites	2,817
Quantitative values	48,127
PSMs, all (including decoys and sub-threshold)	514,154
MS2 identification rate (pxreprise:DEF-ID-RATE)	12.7%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	0.5%

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: acetyl
Instrument vendor: not recorded
Runs / samples: 9 / 9
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: b8b36ebf6016

Modifications

Search engine's name	UNIMOD	Sites
Oxidation on M	UNIMOD:35	1,180
Carbamidomethyl on C	UNIMOD:4	1,000
N6-acetyllysine on K	UNIMOD:1	403
Hydroxylation on P	UNIMOD:35	38
Phosphoserine on S	UNIMOD:21	33
N-acetylalanine on A	UNIMOD:1	27
N-acetylserine on S	UNIMOD:1	15
Acetylation on K	UNIMOD:1	11
Hydroxylation on K	UNIMOD:35	9
Phosphothreonine on T	UNIMOD:21	8
HexNAc on T	UNIMOD:43	5
Asymmetric dimethylarginine on R	UNIMOD:36	4
4-hydroxyproline on P	UNIMOD:35	3
Acetylation on X	UNIMOD:1	3
HexNAc on S	UNIMOD:43	3
N-acetylthreonine on T	UNIMOD:1	3
N6,N6,N6-trimethyllysine on K	UNIMOD:37	3
N6-butyryllysine on K	UNIMOD:1289	3
N6-methyllysine on K	UNIMOD:34	3
Omega-N-methylarginine on R	UNIMOD:34	3
N-acetylcysteine on C	UNIMOD:1	2
N6-succinyllysine on K	—	2
Phosphorylation on S	UNIMOD:21	2
Tele-methylhistidine on H	UNIMOD:34	2
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	1
Allysine on K	UNIMOD:352	1
Cysteine sulfonic acid (-SO3H) on C	UNIMOD:345	1
Dimethylation on K	UNIMOD:36	1
Dimethylation on R	UNIMOD:36	1
Hypusine on K	UNIMOD:379	1
Methylation on R	UNIMOD:34	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N-acetylmethionine on M	UNIMOD:1	1
N-myristoyl glycine on G	UNIMOD:45	1
N6,N6-dimethyllysine on K	UNIMOD:36	1
N6-crotonyllysine on K	—	1
Phosphorylation on T	UNIMOD:21	1
Phosphotyrosine on Y	UNIMOD:21	1
Pros-methylhistidine on H	UNIMOD:34	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: 6903b042e7e4466c, written 2026-10-29T09:39:24+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