Generated summary PXD013640 is a DDA label-free dataset (Homo sapiens) with 16 runs, 16 samples and enrichment: chemical_probe. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 56,309 PSMs, 4,232 peptidoforms and 793 protein groups, and the repository holds 2,856 PTM sites for it. 6 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, 6 warnings and 1 for information

count_mismatch warning
The bundle holds 56309 where the producer reported 56314 (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.

high_contamination warning
61.45% of protein intensity in the worst file, 27.23% median across 16 files (DEF-QC-9 v3.5)

low_core_use warning
12.88 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 6614 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 567 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: 192 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
46 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	56,309
Peptidoforms at 1% FDR	4,232
Protein groups at 1% FDR	793
PTM sites	2,856
Quantitative values	36,544
PSMs, all (including decoys and sub-threshold)	116,121
MS2 identification rate (pxreprise:DEF-ID-RATE)	28.0%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	25.7%

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: chemical_probe
Instrument vendor: not recorded
Runs / samples: 16 / 16
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
Oxidation on M	UNIMOD:35	862
Methylthio on C	UNIMOD:39	528
Deamidation on N	UNIMOD:7	330
Deamidation on Q	UNIMOD:7	221
Hydroxylation on P	UNIMOD:35	83
N-acetylalanine on A	UNIMOD:1	61
Citrullination on R	UNIMOD:7	60
Hydroxylation on N	UNIMOD:35	49
Ammonia loss on N	UNIMOD:385	44
Hydroxylation on K	UNIMOD:35	34
Methylation on K	UNIMOD:34	30
N-acetylserine on S	UNIMOD:1	25
Phosphoserine on S	UNIMOD:21	23
Sodium on E	UNIMOD:30	22
Methylation on R	UNIMOD:34	20
Carbamyl on X	UNIMOD:5	19
Magnesium on D	UNIMOD:956	17
Dimethylation on K	UNIMOD:36	16
N-acetylmethionine on M	UNIMOD:1	14
Acetylation on K	UNIMOD:1	12
Deamidated asparagine on N	UNIMOD:7	12
Magnesium on E	UNIMOD:956	11
Carbamyl on K	UNIMOD:5	9
Dimethylation on R	UNIMOD:36	8
N6,N6,N6-trimethyllysine on K	UNIMOD:37	8
Sodium on D	UNIMOD:30	8
Butyrylation on K	UNIMOD:1289	7
Formylation on K	UNIMOD:122	7
N6-acetyllysine on K	UNIMOD:1	7
N6-methyllysine on K	UNIMOD:34	7
Hydroxybutyrylation on K	—	6
Phosphorylation on S	UNIMOD:21	6
N6,N6-dimethyllysine on K	UNIMOD:36	5
Phosphorylation on T	UNIMOD:21	5
4-hydroxyproline on P	UNIMOD:35	4
Carboxylation on K	UNIMOD:299	4
Tele-methylhistidine on H	UNIMOD:34	4
Acetylation on X	UNIMOD:1	3
Carboxylation on D	UNIMOD:299	3
Carboxylation on E	UNIMOD:299	3
HexNAc on S	UNIMOD:43	3
N-acetylglycine on G	UNIMOD:1	3
N-acetylthreonine on T	UNIMOD:1	3
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	3
Nitrosylation on Y	UNIMOD:354	3
Succinylation on K	UNIMOD:64	3
Water Loss on E	UNIMOD:27	3
Carbamyl on R	UNIMOD:5	2
HexNAc on T	UNIMOD:43	2
N-acetylvaline on V	UNIMOD:1	2
Omega-N-methylarginine on R	UNIMOD:34	2
Phosphothreonine on T	UNIMOD:21	2
Trimethylation on K	UNIMOD:37	2
4-hydroxylysine on K	UNIMOD:35	1
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	1
Asymmetric dimethylarginine on R	UNIMOD:36	1
Crotonylation on K	UNIMOD:1363	1
Malonylation on K	UNIMOD:747	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-crotonyllysine on K	—	1
Phosphotyrosine on Y	UNIMOD:21	1
S-(2-succinyl)cysteine on C	UNIMOD:957	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: 558be41f3850e1f7, written 2026-10-29T09:44:24+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