Generated summary PXD015170 is a DDA label-free dataset (Mus musculus) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 121,033 PSMs, 13,290 peptidoforms and 2,744 protein groups, and the repository holds 4,189 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

count_mismatch warning
The bundle holds 121033 where the producer reported 121034 (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
7.64 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 12610 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6030 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: 179 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
69 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	121,033
Peptidoforms at 1% FDR	13,290
Protein groups at 1% FDR	2,744
PTM sites	4,189
Quantitative values	285,375
PSMs, all (including decoys and sub-threshold)	752,965
MS2 identification rate (pxreprise:DEF-ID-RATE)	21.9%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	1.0%

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: 18 / 18
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	1,675
Oxidation on M	UNIMOD:35	1,123
Phosphoserine on S	UNIMOD:21	218
N-acetylalanine on A	UNIMOD:1	206
Hydroxylation on P	UNIMOD:35	125
N-acetylmethionine on M	UNIMOD:1	103
N-acetylserine on S	UNIMOD:1	92
Acetylation on X	UNIMOD:1	82
Phosphorylation on S	UNIMOD:21	62
Phosphorylation on T	UNIMOD:21	55
Crotonylation on K	UNIMOD:1363	52
4-hydroxyproline on P	UNIMOD:35	34
Phosphothreonine on T	UNIMOD:21	29
N-acetylthreonine on T	UNIMOD:1	20
Hydroxylation on K	UNIMOD:35	19
N6-acetyllysine on K	UNIMOD:1	18
GG (Ubiquitination Site) on K	UNIMOD:121	15
Asymmetric dimethylarginine on R	UNIMOD:36	13
Deamidated asparagine on N	UNIMOD:7	13
Phosphotyrosine on Y	UNIMOD:21	13
N6,N6-dimethyllysine on K	UNIMOD:36	12
Hydroxybutyrylation on K	—	10
Omega-N-methylarginine on R	UNIMOD:34	10
HexNAc on T	UNIMOD:43	8
Methylation on K	UNIMOD:34	8
Phosphorylation on Y	UNIMOD:21	7
N6,N6,N6-trimethyllysine on K	UNIMOD:37	6
Dimethylation on K	UNIMOD:36	5
HexNAc on S	UNIMOD:43	5
N-acetylglycine on G	UNIMOD:1	4
Tele-methylhistidine on H	UNIMOD:34	4
3-hydroxyproline on P	UNIMOD:35	3
Acetylation on K	UNIMOD:1	3
Dimethylation on R	UNIMOD:36	3
Malonylation on K	UNIMOD:747	3
N-acetylvaline on V	UNIMOD:1	3
N6-succinyllysine on K	—	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
5-hydroxylysine on K	UNIMOD:35	2
Butyrylation on K	UNIMOD:1289	2
Dimethylated arginine on R	UNIMOD:36	2
Glutarylation on K	UNIMOD:1848	2
Hydroxyproline on P	UNIMOD:35	2
N-acetylcysteine on C	UNIMOD:1	2
N6-methyllysine on K	UNIMOD:34	2
(3S)-3-hydroxyhistidine on H	—	1
4-hydroxylysine on K	UNIMOD:35	1
Citrulline on R	UNIMOD:7	1
Methylation on R	UNIMOD:34	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N-myristoyl glycine on G	UNIMOD:45	1
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	1
N6-butyryllysine on K	UNIMOD:1289	1
N6-crotonyllysine on K	—	1
N6-glutaryllysine on K	—	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: d306867bc9300942, written 2026-10-29T10:51:26+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