Generated summary PXD057502 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 82,421 PSMs, 5,962 peptidoforms and 2,085 protein groups, and the repository holds 7,777 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 82421 where the producer reported 82424 (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
7.23 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: 82424/583268 = 14.13% 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 51246 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1643 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: 57 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
66 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	82,421
Peptidoforms at 1% FDR	5,962
Protein groups at 1% FDR	2,085
PTM sites	7,777
Quantitative values	79,669
PSMs, all (including decoys and sub-threshold)	1,376,912
MS2 identification rate (pxreprise:DEF-ID-RATE)	14.1%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	1.5%

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: phospho
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: 6ea39b9e1b3a

Modifications

Search engine's name	UNIMOD	Sites
Phosphoserine on S	UNIMOD:21	4,585
Carbamidomethyl on C	UNIMOD:4	1,452
Oxidation on M	UNIMOD:35	659
Phosphothreonine on T	UNIMOD:21	504
N-acetylalanine on A	UNIMOD:1	84
Phosphotyrosine on Y	UNIMOD:21	80
Phosphorylation on S	UNIMOD:21	51
N-acetylserine on S	UNIMOD:1	50
N-acetylmethionine on M	UNIMOD:1	39
Phosphorylation on T	UNIMOD:21	36
Hydroxylation on P	UNIMOD:35	34
Acetylation on X	UNIMOD:1	23
4-hydroxyproline on P	UNIMOD:35	13
N6-acetyllysine on K	UNIMOD:1	11
Omega-N-methylarginine on R	UNIMOD:34	10
N-acetylthreonine on T	UNIMOD:1	9
Acetylation on K	UNIMOD:1	5
Asymmetric dimethylarginine on R	UNIMOD:36	5
HexNAc on S	UNIMOD:43	5
Hydroxylation on K	UNIMOD:35	5
N-acetylglycine on G	UNIMOD:1	5
Tele-methylhistidine on H	UNIMOD:34	5
GG (Ubiquitination Site) on K	UNIMOD:121	4
Methylation on K	UNIMOD:34	4
N-acetylcysteine on C	UNIMOD:1	4
N6,N6-dimethyllysine on K	UNIMOD:36	4
HexNAc on T	UNIMOD:43	3
Methylation on R	UNIMOD:34	3
Glutarylation on K	UNIMOD:1848	2
N6-succinyllysine on K	—	2
Phosphorylation on Y	UNIMOD:21	2
4-carboxyglutamate on E	UNIMOD:299	1
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	1
Butyrylation on K	UNIMOD:1289	1
Crotonylation on K	UNIMOD:1363	1
Deamidated asparagine on N	UNIMOD:7	1
Dimethylation on K	UNIMOD:36	1
Diphosphoserine on S	UNIMOD:898	1
Hydroxybutyrylation on K	—	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-methyllysine on K	UNIMOD:34	1
Pros-methylhistidine on H	UNIMOD:34	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: 7f2a7f357e3b8713, written 2026-10-29T12:13:06+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