Generated summary PXD029116 is a DDA label-free dataset (Homo sapiens) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 66,215 PSMs, 4,135 peptidoforms and 402 protein groups, and the repository holds 3,896 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

low_core_use warning
13.04 avg cores of 32 allowed (S5)

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 28376 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 341 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: 9 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
52 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	66,215
Peptidoforms at 1% FDR	4,135
Protein groups at 1% FDR	402
PTM sites	3,896
Quantitative values	82,441
PSMs, all (including decoys and sub-threshold)	119,388
MS2 identification rate (pxreprise:DEF-ID-RATE)	31.7%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	1.6%

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: 30 / 30
Sample metadata: absent
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	1,135
Hydroxylation on P	UNIMOD:35	507
Deamidation on N	UNIMOD:7	421
Oxidation on M	UNIMOD:35	293
Deamidation on Q	UNIMOD:7	289
4-hydroxyproline on P	UNIMOD:35	133
Ammonia loss on C	UNIMOD:385	97
Citrullination on R	UNIMOD:7	76
Ammonia loss on N	UNIMOD:385	66
Hydroxylation on K	UNIMOD:35	55
Carbamyl on K	UNIMOD:5	50
Carbamyl on X	UNIMOD:5	48
Hydroxylation on N	UNIMOD:35	48
Phosphorylation on S	UNIMOD:21	46
Magnesium on E	UNIMOD:956	45
Sodium on E	UNIMOD:30	30
Magnesium on D	UNIMOD:956	29
Phosphorylation on T	UNIMOD:21	29
Sodium on D	UNIMOD:30	28
Acetylation on K	UNIMOD:1	25
Methylation on K	UNIMOD:34	23
Methylation on R	UNIMOD:34	23
Phosphoserine on S	UNIMOD:21	21
Water Loss on E	UNIMOD:27	20
Formylation on K	UNIMOD:122	16
Carbamyl on R	UNIMOD:5	14
Carbamyl on M	UNIMOD:5	13
Malonylation on K	UNIMOD:747	13
N-acetylalanine on A	UNIMOD:1	13
Calcium on E	UNIMOD:951	12
Carboxylation on E	UNIMOD:299	12
Carboxylation on K	UNIMOD:299	9
3-hydroxyproline on P	UNIMOD:35	8
Carboxylation on D	UNIMOD:299	7
5-hydroxylysine on K	UNIMOD:35	6
Calcium on D	UNIMOD:951	6
Dimethylation on K	UNIMOD:36	6
Dimethylation on R	UNIMOD:36	6
Fe[III] on D	UNIMOD:1870	5
Fe[II] on D	UNIMOD:952	5
Hydroxyproline on P	UNIMOD:35	5
N-acetylserine on S	UNIMOD:1	4
Potassium on D	UNIMOD:530	4
Crotonylation on K	UNIMOD:1363	3
Fe[III] on E	UNIMOD:1870	3
Fe[II] on E	UNIMOD:952	3
GG (Ubiquitination Site) on K	UNIMOD:121	3
Trimethylation on K	UNIMOD:37	3
Acetylation on X	UNIMOD:1	2
Butyrylation on K	UNIMOD:1289	2
Carbamyl on C	UNIMOD:5	2
Citrulline on R	UNIMOD:7	2
Deamidated asparagine on N	UNIMOD:7	2
N-acetylvaline on V	UNIMOD:1	2
Omega-N-methylarginine on R	UNIMOD:34	2
Potassium on E	UNIMOD:530	2
Sulfonation on Y	UNIMOD:40	2
Tele-methylhistidine on H	UNIMOD:34	2
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	1
Asymmetric dimethylarginine on R	UNIMOD:36	1
Hydroxybutyrylation on K	—	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
N6-acetyllysine on K	UNIMOD:1	1
N6-succinyllysine on K	—	1
Phosphorylation on Y	UNIMOD:21	1
Phosphothreonine on T	UNIMOD:21	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: 84728de07f4ad4e4, written 2026-10-29T09:46:02+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