Generated summary PXD022227 is a DDA label-free dataset (Mus musculus) with 35 runs, 35 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 184,016 PSMs, 18,035 peptidoforms and 2,876 protein groups, and the repository holds 9,756 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

high_contamination warning
45.52% of protein intensity in the worst file, 13.58% median across 35 files (DEF-QC-9 v3.5)

low_core_use warning
10 avg cores of 32 allowed (S5)

mbr_kept_exceeds_msms warning
kept MBR 176628 > MSMS 172182 (DEF-MBR-KEPT v1)

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 7726 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3688 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: 436 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
119 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	184,016
Peptidoforms at 1% FDR	18,035
Protein groups at 1% FDR	2,876
PTM sites	9,756
Quantitative values	566,796
PSMs, all (including decoys and sub-threshold)	1,503,377
MS2 identification rate (pxreprise:DEF-ID-RATE)	25.6%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	7.7%

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: 35 / 35
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
Carbamidomethyl on C	UNIMOD:4	5,433
Oxidation on M	UNIMOD:35	2,981
Phosphoserine on S	UNIMOD:21	161
Hydroxylation on P	UNIMOD:35	150
N-acetylalanine on A	UNIMOD:1	113
N6-acetyllysine on K	UNIMOD:1	65
Acetylation on X	UNIMOD:1	61
N-acetylserine on S	UNIMOD:1	50
N-acetylmethionine on M	UNIMOD:1	35
4-hydroxyproline on P	UNIMOD:35	34
Hydroxylation on K	UNIMOD:35	34
Phosphothreonine on T	UNIMOD:21	25
Omega-N-methylarginine on R	UNIMOD:34	18
GG (Ubiquitination Site) on K	UNIMOD:121	16
HexNAc on S	UNIMOD:43	14
Acetylation on K	UNIMOD:1	13
HexNAc on T	UNIMOD:43	13
N6-succinyllysine on K	—	12
Methylation on K	UNIMOD:34	11
Deamidated asparagine on N	UNIMOD:7	10
N6,N6-dimethyllysine on K	UNIMOD:36	9
Asymmetric dimethylarginine on R	UNIMOD:36	8
N6-methyllysine on K	UNIMOD:34	8
Phosphorylation on S	UNIMOD:21	8
N-acetylthreonine on T	UNIMOD:1	7
Dimethylation on R	UNIMOD:36	6
Methylation on R	UNIMOD:34	6
Phosphorylation on T	UNIMOD:21	6
N6,N6,N6-trimethyllysine on K	UNIMOD:37	5
Dimethylation on K	UNIMOD:36	4
N-acetylglycine on G	UNIMOD:1	4
Tele-methylhistidine on H	UNIMOD:34	4
3-hydroxyproline on P	UNIMOD:35	3
Crotonylation on K	UNIMOD:1363	3
N-acetylcysteine on C	UNIMOD:1	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Dimethylated arginine on R	UNIMOD:36	2
Glutarylation on K	UNIMOD:1848	2
N6-malonyllysine on K	—	2
5-hydroxylysine on K	UNIMOD:35	1
Allysine on K	UNIMOD:352	1
Citrulline on R	UNIMOD:7	1
Cysteine sulfenic acid (-SOH) on C	UNIMOD:35	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-butyryllysine on K	UNIMOD:1289	1
N6-isonicotinyllysine on K	UNIMOD:697	1
N6-methacryllysine on K	—	1
Phosphorylation on Y	UNIMOD:21	1
Phosphotyrosine on Y	UNIMOD:21	1
S-palmitoyl cysteine on C	UNIMOD:47	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: afc62147d98af269, written 2026-10-29T11:27:39+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