Generated summary PXD010820 is a DDA label-free dataset (Homo sapiens) 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 259,817 PSMs, 27,693 peptidoforms and 3,369 protein groups, and the repository holds 16,115 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 259817 where the producer reported 259851 (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
15.33 avg cores of 32 allowed (S5)

occupancy_not_stored warning
Of 56017 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6092 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).

sdrf_uncoded warning
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: Cell culture. Match on it as text; it has not been mapped to a term.

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: 1493 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
59 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	259,817
Peptidoforms at 1% FDR	27,693
Protein groups at 1% FDR	3,369
PTM sites	16,115
Quantitative values	326,050
PSMs, all (including decoys and sub-threshold)	1,024,757
MS2 identification rate (pxreprise:DEF-ID-RATE)	62.9%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	1.4%

How it was measured

Organism searched: Homo sapiens (the protein database's organism, not a statement about the samples)
Acquisition: DDA
Quantification: label_free
Labelling: none
Enrichment: none
Instrument vendor: Thermo
Runs / samples: 12 / 12
Sample metadata: trusted
Search engine: MetaMorpheus 1.1.12
Protein database: UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
Pipeline commit: 5aec9eb024d8

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	4,370
Deamidation on N	UNIMOD:7	1,368
Deamidation on Q	UNIMOD:7	1,330
Oxidation on M	UNIMOD:35	1,284
Carbamyl on X	UNIMOD:5	951
Formylation on K	UNIMOD:122	779
Carbamyl on M	UNIMOD:5	575
Acetylation on K	UNIMOD:1	380
Hydroxylation on P	UNIMOD:35	318
Citrullination on R	UNIMOD:7	297
Ammonia loss on N	UNIMOD:385	292
N-acetylalanine on A	UNIMOD:1	270
Methylation on K	UNIMOD:34	182
Sodium on E	UNIMOD:30	146
Phosphoserine on S	UNIMOD:21	135
Hydroxylation on N	UNIMOD:35	132
Magnesium on E	UNIMOD:956	130
Ammonia loss on C	UNIMOD:385	122
Carboxylation on E	UNIMOD:299	117
Trimethylation on K	UNIMOD:37	109
Methylation on R	UNIMOD:34	101
Sodium on D	UNIMOD:30	99
Carboxylation on D	UNIMOD:299	97
N6-acetyllysine on K	UNIMOD:1	95
Acetylation on X	UNIMOD:1	89
N-acetylserine on S	UNIMOD:1	85
Dimethylation on K	UNIMOD:36	84
Carbamyl on K	UNIMOD:5	81
Magnesium on D	UNIMOD:956	80
Hydroxylation on K	UNIMOD:35	78
Dimethylation on R	UNIMOD:36	69
N-acetylmethionine on M	UNIMOD:1	58
GG (Ubiquitination Site) on K	UNIMOD:121	54
Carbamyl on R	UNIMOD:5	53
Malonylation on K	UNIMOD:747	52
Calcium on E	UNIMOD:951	50
Nitrosylation on Y	UNIMOD:354	49
Phosphorylation on S	UNIMOD:21	48
Water Loss on E	UNIMOD:27	46
Glutarylation on K	UNIMOD:1848	43
Carbamyl on C	UNIMOD:5	41
Calcium on D	UNIMOD:951	39
Fe[III] on E	UNIMOD:1870	39
Nitrosylation on C	UNIMOD:275	36
Crotonylation on K	UNIMOD:1363	32
Potassium on D	UNIMOD:530	31
Butyrylation on K	UNIMOD:1289	29
Succinylation on K	UNIMOD:64	29
Asymmetric dimethylarginine on R	UNIMOD:36	28
Hydroxybutyrylation on K	—	28
Phosphorylation on T	UNIMOD:21	28
HexNAc on T	UNIMOD:43	26
Phosphothreonine on T	UNIMOD:21	26
Omega-N-methylarginine on R	UNIMOD:34	25
Fe[III] on D	UNIMOD:1870	24
N6-methyllysine on K	UNIMOD:34	23
Carboxylation on K	UNIMOD:299	22
N-acetylthreonine on T	UNIMOD:1	21
N6,N6-dimethyllysine on K	UNIMOD:36	19
Potassium on E	UNIMOD:530	19
HexNAc on S	UNIMOD:43	18
N6,N6,N6-trimethyllysine on K	UNIMOD:37	18
4-hydroxyproline on P	UNIMOD:35	14
Fe[II] on D	UNIMOD:952	13
Fe[II] on E	UNIMOD:952	13
N6-crotonyllysine on K	—	10
N6-glutaryllysine on K	—	8
N6-succinyllysine on K	—	8
Deamidated asparagine on N	UNIMOD:7	7
N-acetylglycine on G	UNIMOD:1	7
N5-methylglutamine on Q	UNIMOD:34	6
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	6
Phosphotyrosine on Y	UNIMOD:21	6
Sulfonation on Y	UNIMOD:40	6
Hydroxyproline on P	UNIMOD:35	5
N-acetylvaline on V	UNIMOD:1	5
N6-butyryllysine on K	UNIMOD:1289	5
Phosphorylation on Y	UNIMOD:21	4
Tele-methylhistidine on H	UNIMOD:34	4
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Dimethylated arginine on R	UNIMOD:36	2
N-acetylcysteine on C	UNIMOD:1	2
N-myristoyl glycine on G	UNIMOD:45	2
N6-malonyllysine on K	—	2
3'-nitrotyrosine on Y	—	1
5-hydroxylysine on K	UNIMOD:35	1
Deamidated glutamine on Q	UNIMOD:7	1
Diphthamide on H	UNIMOD:375	1
HexNAc on Nxs	UNIMOD:43	1
Leucine methyl ester on L	UNIMOD:34	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-benzoyllysine on K	UNIMOD:136	1
N6-methacryllysine on K	—	1
N6-propionyllysine on K	UNIMOD:58	1
Pros-methylhistidine on H	UNIMOD:34	1
S-nitrosocysteine on C	UNIMOD:275	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: d84f9e1de2d8850f, written 2026-10-29T10:39:53+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