Generated summary PXD012754 is a DDA label-free dataset (Mus musculus) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 11,842 PSMs, 4,299 peptidoforms and 780 protein groups, and the repository holds 2,140 PTM sites for it. 8 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, 8 warnings and 0 for information

calibration_failed warning
GPTMD/search ran on uncalibrated spectra (S7)

high_contamination warning
39.22% of protein intensity in the worst file, 17.19% median across 10 files (DEF-QC-9 v3.5)

low_core_use warning
15.56 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: 11842/354988 = 3.34% of MS2 identified (S3)

mbr_kept_exceeds_msms warning
kept MBR 13649 > MSMS 10428 (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 3134 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 425 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: 93 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.

What was found

PSMs at 1% FDR	11,842
Peptidoforms at 1% FDR	4,299
Protein groups at 1% FDR	780
PTM sites	2,140
Quantitative values	40,344
PSMs, all (including decoys and sub-threshold)	24,089
MS2 identification rate (pxreprise:DEF-ID-RATE)	3.3%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	18.2%

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: 10 / 10
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	753
Deamidation on N	UNIMOD:7	154
Oxidation on M	UNIMOD:35	130
Hydroxylation on P	UNIMOD:35	113
Sodium on E	UNIMOD:30	110
Deamidation on Q	UNIMOD:7	100
Sodium on D	UNIMOD:30	62
N-acetylalanine on A	UNIMOD:1	47
4-hydroxyproline on P	UNIMOD:35	41
Calcium on E	UNIMOD:951	32
Magnesium on E	UNIMOD:956	32
Ammonia loss on N	UNIMOD:385	27
Carbamyl on M	UNIMOD:5	27
Acetylation on K	UNIMOD:1	22
N-acetylserine on S	UNIMOD:1	21
Hydroxylation on K	UNIMOD:35	20
Methylation on K	UNIMOD:34	18
Carbamyl on X	UNIMOD:5	16
Succinylation on K	UNIMOD:64	16
Citrullination on R	UNIMOD:7	15
Water Loss on E	UNIMOD:27	14
Acetylation on X	UNIMOD:1	13
N6-acetyllysine on K	UNIMOD:1	12
Phosphoserine on S	UNIMOD:21	10
Hydroxylation on N	UNIMOD:35	7
Methylation on R	UNIMOD:34	7
Phosphorylation on T	UNIMOD:21	7
Calcium on D	UNIMOD:951	6
Formylation on K	UNIMOD:122	6
Magnesium on D	UNIMOD:956	6
N-acetylthreonine on T	UNIMOD:1	6
N6,N6,N6-trimethyllysine on K	UNIMOD:37	6
N6-methyllysine on K	UNIMOD:34	6
Phosphorylation on S	UNIMOD:21	6
Ammonia loss on C	UNIMOD:385	5
Carbamyl on K	UNIMOD:5	5
Deamidated asparagine on N	UNIMOD:7	4
Glutarylation on K	UNIMOD:1848	4
N6,N6-dimethyllysine on K	UNIMOD:36	4
Tele-methylhistidine on H	UNIMOD:34	4
Carbamyl on R	UNIMOD:5	3
GG (Ubiquitination Site) on K	UNIMOD:121	3
Trimethylation on K	UNIMOD:37	3
Asymmetric dimethylarginine on R	UNIMOD:36	2
Hydroxybutyrylation on K	—	2
N-acetylglycine on G	UNIMOD:1	2
N-acetylvaline on V	UNIMOD:1	2
3-hydroxyproline on P	UNIMOD:35	1
Carbamyl on C	UNIMOD:5	1
Crotonylation on K	UNIMOD:1363	1
Dimethylation on K	UNIMOD:36	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylcysteine on C	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N-acetylmethionine on M	UNIMOD:1	1
Nitrosylation on C	UNIMOD:275	1
Omega-N-methylarginine on R	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: 7e23bcb799d1bbb7, written 2026-10-29T09:52:55+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