Generated summary PXD058082 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 42,223 PSMs, 5,087 peptidoforms and 1,203 protein groups, and the repository holds 1,820 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

low_core_use warning
14.85 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: 42223/329646 = 12.81% of MS2 identified (S3)

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 3012 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 138 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: 98 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.

collapsed_duplicate_rows info
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 2 identifier(s), 7 row(s) dropped, e.g. PXD058082:A0A1W2P6Q8;A0A1W2P7H4;A0A1W2P7S8;A0A1W2P7Z8;A0A1W2P855;Q6A068 written 6 times; quant_values: 38 identifier(s), 145 row(s) dropped, e.g. PXD058082:Lung_PM25_MM_High_D10X_N1:label_free:protein_group:PXD058082:A0A1W2P6Q8;A0A1W2P7H4;A0A1W2P7S8;A0A1W2P7Z8;A0A1W2P855;Q6A068:QuantProject:DEF-PROT-INT written 6 times. The full list is in bundle.json under collapsed_duplicates.

What was found

PSMs at 1% FDR	42,223
Peptidoforms at 1% FDR	5,087
Protein groups at 1% FDR	1,203
PTM sites	1,820
Quantitative values	107,982
PSMs, all (including decoys and sub-threshold)	57,058
MS2 identification rate (pxreprise:DEF-ID-RATE)	12.8%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	0.8%

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: 15 / 15
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 0ba5e4c3fd33

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	1,049
Oxidation on M	UNIMOD:35	325
Calcium on D	UNIMOD:951	106
Calcium on E	UNIMOD:951	82
Deamidation on N	UNIMOD:7	61
Deamidation on Q	UNIMOD:7	24
Hydroxylation on P	UNIMOD:35	24
Water Loss on E	UNIMOD:27	19
N6-acetyllysine on K	UNIMOD:1	15
Magnesium on D	UNIMOD:956	14
Hydroxylation on N	UNIMOD:35	9
Hydroxylation on K	UNIMOD:35	8
Tele-methylhistidine on H	UNIMOD:34	5
Deamidated asparagine on N	UNIMOD:7	4
N-acetylalanine on A	UNIMOD:1	4
N-acetylmethionine on M	UNIMOD:1	4
N6,N6,N6-trimethyllysine on K	UNIMOD:37	4
Citrullination on R	UNIMOD:7	3
HexNAc on T	UNIMOD:43	3
Magnesium on E	UNIMOD:956	3
N-acetylserine on S	UNIMOD:1	3
N6-methyllysine on K	UNIMOD:34	3
Phosphoserine on S	UNIMOD:21	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Acetylation on K	UNIMOD:1	2
Carbamyl on X	UNIMOD:5	2
Formylation on K	UNIMOD:122	2
HexNAc on S	UNIMOD:43	2
Methylation on K	UNIMOD:34	2
N-acetylglycine on G	UNIMOD:1	2
N6,N6-dimethyllysine on K	UNIMOD:36	2
Phosphorylation on T	UNIMOD:21	2
Acetylation on X	UNIMOD:1	1
Carbamyl on M	UNIMOD:5	1
Dimethylation on K	UNIMOD:36	1
Methylation on R	UNIMOD:34	1
N-acetylvaline on V	UNIMOD:1	1
N-myristoyl glycine on G	UNIMOD:45	1
N6-crotonyllysine on K	—	1
Phosphorylation on Y	UNIMOD:21	1
Succinylation on K	UNIMOD:64	1
Symmetric dimethylarginine on R	UNIMOD:36	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: 7bae2533b1705414, written 2026-10-29T09:51:51+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