Generated summary PXD017944 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 69,785 PSMs, 9,263 peptidoforms and 879 protein groups, and the repository holds 5,405 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
16.43% of protein intensity in the worst file, 6.18% median across 20 files (DEF-QC-9 v3.5)

low_core_use warning
13.46 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 21642 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1388 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: 329 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
12 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	69,785
Peptidoforms at 1% FDR	9,263
Protein groups at 1% FDR	879
PTM sites	5,405
Quantitative values	155,727
PSMs, all (including decoys and sub-threshold)	107,280
MS2 identification rate (pxreprise:DEF-ID-RATE)	46.8%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	5.9%

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: 20 / 20
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
Pipeline commit: 5aec9eb024d8

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	1,864
Oxidation on M	UNIMOD:35	646
Deamidation on N	UNIMOD:7	340
Hydroxylation on P	UNIMOD:35	323
Sodium on E	UNIMOD:30	291
Deamidation on Q	UNIMOD:7	240
Sodium on D	UNIMOD:30	170
Ammonia loss on C	UNIMOD:385	129
Ammonia loss on N	UNIMOD:385	102
4-hydroxyproline on P	UNIMOD:35	70
Carbamyl on X	UNIMOD:5	57
Hydroxylation on N	UNIMOD:35	50
N-acetylalanine on A	UNIMOD:1	49
Hydroxylation on K	UNIMOD:35	47
Phosphorylation on S	UNIMOD:21	39
Magnesium on E	UNIMOD:956	31
Magnesium on D	UNIMOD:956	28
N-acetylmethionine on M	UNIMOD:1	28
Water Loss on E	UNIMOD:27	27
Calcium on D	UNIMOD:951	24
Citrullination on R	UNIMOD:7	24
Methylation on K	UNIMOD:34	22
Acetylation on X	UNIMOD:1	21
N-acetylserine on S	UNIMOD:1	20
Calcium on E	UNIMOD:951	19
Phosphorylation on T	UNIMOD:21	18
Phosphoserine on S	UNIMOD:21	18
N5-methylglutamine on Q	UNIMOD:34	17
Carbamyl on M	UNIMOD:5	16
Acetylation on K	UNIMOD:1	13
Fe[II] on E	UNIMOD:952	13
N6-acetyllysine on K	UNIMOD:1	8
Methylation on R	UNIMOD:34	7
N-acetylthreonine on T	UNIMOD:1	7
Sulfonation on Y	UNIMOD:40	7
Dimethylation on K	UNIMOD:36	6
Malonylation on K	UNIMOD:747	6
Deamidated asparagine on N	UNIMOD:7	5
N6,N6,N6-trimethyllysine on K	UNIMOD:37	5
N6,N6-dimethyllysine on K	UNIMOD:36	5
Carbamyl on K	UNIMOD:5	4
Crotonylation on K	UNIMOD:1363	4
Phosphorylation on Y	UNIMOD:21	4
Potassium on D	UNIMOD:530	4
Potassium on E	UNIMOD:530	4
Pros-methylhistidine on H	UNIMOD:34	4
Tele-methylhistidine on H	UNIMOD:34	4
3-hydroxyproline on P	UNIMOD:35	3
5-hydroxylysine on K	UNIMOD:35	3
Carbamyl on R	UNIMOD:5	3
HexNAc on S	UNIMOD:43	3
N-acetylcysteine on C	UNIMOD:1	3
N6-methyllysine on K	UNIMOD:34	3
Omega-N-methylarginine on R	UNIMOD:34	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Allysine on K	UNIMOD:352	2
Carbamyl on C	UNIMOD:5	2
HexNAc on T	UNIMOD:43	2
Sulfotyrosine on Y	UNIMOD:40	2
Butyrylation on K	UNIMOD:1289	1
Fe[II] on D	UNIMOD:952	1
GG (Ubiquitination Site) on K	UNIMOD:121	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N-acetylglycine on G	UNIMOD:1	1
N-acetylvaline on V	UNIMOD:1	1
Phosphothreonine on T	UNIMOD:21	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: 3cd52dd1b39472d8, written 2026-10-29T09:48:26+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