Generated summary PXD009212 is a DDA label-free dataset (Rattus norvegicus) with 57 runs, 57 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 195,142 PSMs, 12,844 peptidoforms and 1,711 protein groups, and the repository holds 5,753 PTM sites for it. 7 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, 7 warnings and 1 for information

high_contamination warning
23.55% of protein intensity in the worst file, 2.69% median across 57 files (DEF-QC-9 v3.5)

low_core_use warning
11.75 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: 195142/1912914 = 10.20% of MS2 identified (S3)

mbr_kept_exceeds_msms warning
kept MBR 150475 > MSMS 93530 (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 12705 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1744 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: 876 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
9 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	195,142
Peptidoforms at 1% FDR	12,844
Protein groups at 1% FDR	1,711
PTM sites	5,753
Quantitative values	459,184
PSMs, all (including decoys and sub-threshold)	219,973
MS2 identification rate (pxreprise:DEF-ID-RATE)	10.2%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	2.8%

How it was measured

Organism searched: Rattus norvegicus (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: 57 / 57
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000002494_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 28f7d3fbb2aa

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	2,542
Oxidation on M	UNIMOD:35	1,183
Deamidation on N	UNIMOD:7	576
Deamidation on Q	UNIMOD:7	181
Methylation on K	UNIMOD:34	141
Hydroxylation on P	UNIMOD:35	132
Hydroxylation on N	UNIMOD:35	83
Methylation on R	UNIMOD:34	82
N-acetylalanine on A	UNIMOD:1	69
Phosphoserine on S	UNIMOD:21	61
GG (Ubiquitination Site) on K	UNIMOD:121	55
Carbamyl on X	UNIMOD:5	53
Carbamyl on M	UNIMOD:5	52
Ammonia loss on N	UNIMOD:385	46
Ammonia loss on C	UNIMOD:385	42
Citrullination on R	UNIMOD:7	40
Hydroxylation on K	UNIMOD:35	39
Acetylation on X	UNIMOD:1	35
N-acetylserine on S	UNIMOD:1	22
Dimethylation on R	UNIMOD:36	16
N-acetylmethionine on M	UNIMOD:1	16
4-hydroxyproline on P	UNIMOD:35	14
Phosphorylation on T	UNIMOD:21	14
N6-acetyllysine on K	UNIMOD:1	12
Carbamyl on K	UNIMOD:5	10
N6,N6,N6-trimethyllysine on K	UNIMOD:37	10
Phosphothreonine on T	UNIMOD:21	10
Acetylation on K	UNIMOD:1	8
Omega-N-methylarginine on R	UNIMOD:34	8
Phosphorylation on S	UNIMOD:21	7
Deamidated asparagine on N	UNIMOD:7	6
N-acetylthreonine on T	UNIMOD:1	5
Trimethylation on K	UNIMOD:37	5
Asymmetric dimethylarginine on R	UNIMOD:36	4
Dimethylation on K	UNIMOD:36	4
Glutarylation on K	UNIMOD:1848	4
N-acetylglycine on G	UNIMOD:1	4
Tele-methylhistidine on H	UNIMOD:34	4
Butyrylation on K	UNIMOD:1289	3
Carbamyl on R	UNIMOD:5	3
Phosphorylation on Y	UNIMOD:21	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Citrulline on R	UNIMOD:7	2
Dimethylated arginine on R	UNIMOD:36	2
N-acetylvaline on V	UNIMOD:1	2
N6,N6-dimethyllysine on K	UNIMOD:36	2
N6-methyllysine on K	UNIMOD:34	2
N6-succinyllysine on K	—	2
Nitrosylation on Y	UNIMOD:354	2
Symmetric dimethylarginine on R	UNIMOD:36	2
Deamidated glutamine on Q	UNIMOD:7	1
HexNAc on S	UNIMOD:43	1
HexNAc on T	UNIMOD:43	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N-myristoyl glycine on G	UNIMOD:45	1
N6-glutaryllysine on K	—	1
Phosphotyrosine on Y	UNIMOD:21	1
Sodium on D	UNIMOD:30	1
Succinylation on K	UNIMOD:64	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: f70e9d7850ed82d6, written 2026-10-29T09:37:27+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