Generated summary PXD037230 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 303,336 PSMs, 15,627 peptidoforms and 2,283 protein groups, and the repository holds 9,419 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 303336 where the producer reported 303340 (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
10.72 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 11201 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2111 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: 493 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
182 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	303,336
Peptidoforms at 1% FDR	15,627
Protein groups at 1% FDR	2,283
PTM sites	9,419
Quantitative values	229,156
PSMs, all (including decoys and sub-threshold)	2,276,413
MS2 identification rate (pxreprise:DEF-ID-RATE)	20.6%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	1.9%

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: 12 / 12
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 0095bcefc3f5

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	5,539
Oxidation on M	UNIMOD:35	2,482
Hydroxylation on P	UNIMOD:35	260
Phosphoserine on S	UNIMOD:21	243
N-acetylalanine on A	UNIMOD:1	96
4-hydroxyproline on P	UNIMOD:35	90
Acetylation on X	UNIMOD:1	53
N-acetylmethionine on M	UNIMOD:1	47
Hydroxylation on K	UNIMOD:35	37
N6-acetyllysine on K	UNIMOD:1	37
N-acetylserine on S	UNIMOD:1	32
Phosphothreonine on T	UNIMOD:21	31
HexNAc on T	UNIMOD:43	19
Omega-N-methylarginine on R	UNIMOD:34	18
GG (Ubiquitination Site) on K	UNIMOD:121	17
HexNAc on S	UNIMOD:43	17
Methylation on K	UNIMOD:34	16
N6-glutaryllysine on K	—	15
N-acetylthreonine on T	UNIMOD:1	14
Phosphotyrosine on Y	UNIMOD:21	14
Phosphorylation on S	UNIMOD:21	13
Phosphorylation on T	UNIMOD:21	13
N6,N6-dimethyllysine on K	UNIMOD:36	12
N6-methyllysine on K	UNIMOD:34	12
N6-succinyllysine on K	—	11
Acetylation on K	UNIMOD:1	10
Asymmetric dimethylarginine on R	UNIMOD:36	10
Trimethylation on K	UNIMOD:37	9
Deamidated asparagine on N	UNIMOD:7	8
N6,N6,N6-trimethyllysine on K	UNIMOD:37	7
5-hydroxylysine on K	UNIMOD:35	6
3-hydroxyproline on P	UNIMOD:35	5
Dimethylation on R	UNIMOD:36	5
Methylation on R	UNIMOD:34	5
N-myristoyl glycine on G	UNIMOD:45	4
Pros-methylhistidine on H	UNIMOD:34	4
Tele-methylhistidine on H	UNIMOD:34	4
Allysine on K	UNIMOD:352	3
N-acetylvaline on V	UNIMOD:1	3
Sulfotyrosine on Y	UNIMOD:40	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Dimethylated arginine on R	UNIMOD:36	2
Dimethylation on K	UNIMOD:36	2
N-acetylcysteine on C	UNIMOD:1	2
N-acetylglycine on G	UNIMOD:1	2
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	2
4-hydroxylysine on K	UNIMOD:35	1
Butyrylation on K	UNIMOD:1289	1
Citrulline on R	UNIMOD:7	1
Cysteine sulfinic acid (-SO2H) on C	UNIMOD:425	1
Glutarylation on K	UNIMOD:1848	1
Hydroxybutyrylation on K	—	1
Hydroxyproline on P	UNIMOD:35	1
Malonylation on K	UNIMOD:747	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
Phosphorylation on Y	UNIMOD:21	1
Succinylation on K	UNIMOD:64	1
Symmetric dimethylarginine on R	UNIMOD:36	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: e0f58944531b149f, written 2026-10-29T10:18:08+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