Generated summary PXD012213 is a DDA label-free dataset (Homo sapiens) with 26 runs, 26 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 193,217 PSMs, 4,385 peptidoforms and 320 protein groups, and the repository holds 4,786 PTM sites for it. 4 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, 4 warnings and 1 for information

count_mismatch warning
The bundle holds 193217 where the producer reported 193218 (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.

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 36837 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 13 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: 675 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
71 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	193,217
Peptidoforms at 1% FDR	4,385
Protein groups at 1% FDR	320
PTM sites	4,786
Quantitative values	143,760
PSMs, all (including decoys and sub-threshold)	298,950
MS2 identification rate (pxreprise:DEF-ID-RATE)	31.8%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	1.2%

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: not recorded
Runs / samples: 26 / 26
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 0ba5e4c3fd33

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	1,156
Oxidation on M	UNIMOD:35	538
Deamidation on N	UNIMOD:7	306
Sodium on E	UNIMOD:30	254
Deamidation on Q	UNIMOD:7	220
Sodium on D	UNIMOD:30	201
Calcium on E	UNIMOD:951	175
Calcium on D	UNIMOD:951	141
Fe[II] on E	UNIMOD:952	136
Ammonia loss on N	UNIMOD:385	129
Magnesium on E	UNIMOD:956	125
Hydroxylation on P	UNIMOD:35	119
Magnesium on D	UNIMOD:956	108
Fe[II] on D	UNIMOD:952	107
Methylation on R	UNIMOD:34	94
Hydroxylation on N	UNIMOD:35	73
Methylation on K	UNIMOD:34	71
Potassium on E	UNIMOD:530	57
Citrullination on R	UNIMOD:7	56
Carboxylation on E	UNIMOD:299	44
Potassium on D	UNIMOD:530	44
Hydroxylation on K	UNIMOD:35	43
Water Loss on E	UNIMOD:27	35
Ammonia loss on C	UNIMOD:385	33
Carbamyl on X	UNIMOD:5	30
Formylation on K	UNIMOD:122	26
Dimethylation on R	UNIMOD:36	23
Phosphoserine on S	UNIMOD:21	21
Carbamyl on K	UNIMOD:5	18
Fe[III] on D	UNIMOD:1870	17
Fe[III] on E	UNIMOD:1870	17
Dimethylation on K	UNIMOD:36	16
N6-crotonyllysine on K	—	14
Acetylation on K	UNIMOD:1	13
N6-isonicotinyllysine on K	UNIMOD:697	13
Trimethylation on K	UNIMOD:37	10
Carbamyl on R	UNIMOD:5	9
GG (Ubiquitination Site) on K	UNIMOD:121	9
Phosphorylation on S	UNIMOD:21	8
Carboxylation on D	UNIMOD:299	7
N6-acetyllysine on K	UNIMOD:1	6
Carbamyl on C	UNIMOD:5	5
Phosphothreonine on T	UNIMOD:21	5
Succinylation on K	UNIMOD:64	5
4-hydroxyproline on P	UNIMOD:35	4
Glutarylation on K	UNIMOD:1848	4
HexNAc on T	UNIMOD:43	4
Hydroxybutyrylation on K	—	4
Phosphorylation on T	UNIMOD:21	4
Zinc on E	UNIMOD:954	4
Hydroxyproline on P	UNIMOD:35	3
Nitrosylation on C	UNIMOD:275	3
4-carboxyglutamate on E	UNIMOD:299	2
Carbamyl on M	UNIMOD:5	2
Crotonylation on K	UNIMOD:1363	2
Nitrosylation on Y	UNIMOD:354	2
Phosphorylation on Y	UNIMOD:21	2
Phosphotyrosine on Y	UNIMOD:21	2
Sulfonation on Y	UNIMOD:40	2
Tele-methylhistidine on H	UNIMOD:34	2
Zinc on D	UNIMOD:954	2
(3R)-3-hydroxyaspartate on D	UNIMOD:35	1
Carboxylation on K	UNIMOD:299	1
Cu[I] on D	UNIMOD:531	1
Cu[I] on E	UNIMOD:531	1
HexNAc on S	UNIMOD:43	1
Malonylation on K	UNIMOD:747	1
N-acetylalanine on A	UNIMOD:1	1
N6-succinyllysine on K	—	1
Omega-N-methylarginine on R	UNIMOD:34	1
S-cysteinyl cysteine on C	UNIMOD:312	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: c43d19b1b11dd220, written 2026-10-29T09:27:47+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