Generated summary PXD028852 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 88,611 PSMs, 27,920 peptidoforms and 2,823 protein groups, and the repository holds 8,248 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

high_contamination warning
67.70% of protein intensity in the worst file, 9.32% median across 20 files (DEF-QC-9 v3.5)

low_core_use warning
14.63 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 5664 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1240 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: 63 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
6 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	88,611
Peptidoforms at 1% FDR	27,920
Protein groups at 1% FDR	2,823
PTM sites	8,248
Quantitative values	185,101
PSMs, all (including decoys and sub-threshold)	185,248
MS2 identification rate (pxreprise:DEF-ID-RATE)	62.0%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	4.0%

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: proximity_labelling
Instrument vendor: not recorded
Runs / samples: 20 / 20
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	3,713
Oxidation on M	UNIMOD:35	2,854
Phosphoserine on S	UNIMOD:21	139
Deamidation on Q	UNIMOD:7	131
N-acetylalanine on A	UNIMOD:1	131
Deamidation on N	UNIMOD:7	126
Ammonia loss on N	UNIMOD:385	78
N-acetylmethionine on M	UNIMOD:1	68
Hydroxylation on P	UNIMOD:35	62
Acetylation on X	UNIMOD:1	58
Fe[III] on D	UNIMOD:1870	58
Fe[II] on D	UNIMOD:952	51
N-acetylserine on S	UNIMOD:1	50
Fe[III] on E	UNIMOD:1870	49
Fe[II] on E	UNIMOD:952	49
Ammonia loss on C	UNIMOD:385	40
Hydroxylation on N	UNIMOD:35	40
Hydroxylation on K	UNIMOD:35	22
Citrullination on R	UNIMOD:7	20
Methylation on K	UNIMOD:34	18
Phosphothreonine on T	UNIMOD:21	18
Phosphorylation on S	UNIMOD:21	17
Methylation on R	UNIMOD:34	16
Acetylation on K	UNIMOD:1	12
N6,N6-dimethyllysine on K	UNIMOD:36	10
4-hydroxyproline on P	UNIMOD:35	9
Calcium on E	UNIMOD:951	9
N-acetylthreonine on T	UNIMOD:1	9
N6,N6,N6-trimethyllysine on K	UNIMOD:37	8
Omega-N-methylarginine on R	UNIMOD:34	8
GG (Ubiquitination Site) on K	UNIMOD:121	7
Phosphorylation on T	UNIMOD:21	6
Water Loss on E	UNIMOD:27	6
Asymmetric dimethylarginine on R	UNIMOD:36	5
Carboxylation on E	UNIMOD:299	5
Dimethylation on R	UNIMOD:36	5
N6-methyllysine on K	UNIMOD:34	5
Sodium on D	UNIMOD:30	5
Dimethylation on K	UNIMOD:36	4
N-acetylglycine on G	UNIMOD:1	4
N-myristoyl glycine on G	UNIMOD:45	4
N6-acetyllysine on K	UNIMOD:1	4
Sodium on E	UNIMOD:30	4
Deamidated asparagine on N	UNIMOD:7	3
Magnesium on E	UNIMOD:956	3
Phosphorylation on Y	UNIMOD:21	3
Crotonylation on K	UNIMOD:1363	2
Formylation on K	UNIMOD:122	2
Malonylation on K	UNIMOD:747	2
N-acetylcysteine on C	UNIMOD:1	2
Tele-methylhistidine on H	UNIMOD:34	2
(3S)-3-hydroxyhistidine on H	—	1
3-hydroxyproline on P	UNIMOD:35	1
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	1
Calcium on D	UNIMOD:951	1
Carbamyl on K	UNIMOD:5	1
Carboxylation on K	UNIMOD:299	1
Diphthamide on H	UNIMOD:375	1
Glutarylation on K	UNIMOD:1848	1
HexNAc on S	UNIMOD:43	1
Magnesium on D	UNIMOD:956	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-acetyl-N6-methyllysine on K	—	1
Nitrosylation on Y	UNIMOD:354	1
Potassium on E	UNIMOD:530	1
Pros-methylhistidine on H	UNIMOD:34	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: 13a69f7a4f0d744f, written 2026-10-29T09:41:03+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