Generated summary PXD007049 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 22,417 PSMs, 3,745 peptidoforms and 781 protein groups, and the repository holds 1,827 PTM sites for it. 7 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, 7 warnings and 1 for information

count_mismatch warning
The bundle holds 22417 where the producer reported 22418 (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.

cysteine_poor warning
0.69% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)

high_contamination warning
46.75% of protein intensity in the worst file, 35.78% median across 12 files (DEF-QC-9 v3.5)

low_core_use warning
10.21 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 6499 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 327 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: 42 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
11 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	22,417
Peptidoforms at 1% FDR	3,745
Protein groups at 1% FDR	781
PTM sites	1,827
Quantitative values	44,579
PSMs, all (including decoys and sub-threshold)	77,079
MS2 identification rate (pxreprise:DEF-ID-RATE)	17.0%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	31.3%

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: affinity_purification
Instrument vendor: not recorded
Runs / samples: 12 / 12
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
Pipeline commit: 9df4ce025f23

Modifications

Search engine's name	UNIMOD	Sites
Oxidation on M	UNIMOD:35	348
Deamidation on N	UNIMOD:7	159
Fe[III] on E	UNIMOD:1870	130
Deamidation on Q	UNIMOD:7	118
Fe[III] on D	UNIMOD:1870	85
Carbamidomethyl on C	UNIMOD:4	81
Hydroxylation on P	UNIMOD:35	71
Fe[II] on E	UNIMOD:952	46
Hydroxylation on K	UNIMOD:35	44
Ammonia loss on N	UNIMOD:385	42
Hydroxylation on N	UNIMOD:35	42
N-acetylalanine on A	UNIMOD:1	25
Fe[II] on D	UNIMOD:952	23
Methylation on K	UNIMOD:34	20
Citrullination on R	UNIMOD:7	15
Methylation on R	UNIMOD:34	15
N-acetylmethionine on M	UNIMOD:1	14
N-acetylserine on S	UNIMOD:1	10
N6,N6-dimethyllysine on K	UNIMOD:36	10
GG (Ubiquitination Site) on K	UNIMOD:121	9
Phosphorylation on T	UNIMOD:21	9
Phosphoserine on S	UNIMOD:21	9
Dimethylation on R	UNIMOD:36	8
N6,N6,N6-trimethyllysine on K	UNIMOD:37	8
Carbamyl on X	UNIMOD:5	7
Acetylation on K	UNIMOD:1	5
Dimethylation on K	UNIMOD:36	5
Omega-N-methylarginine on R	UNIMOD:34	5
Phosphorylation on S	UNIMOD:21	5
Nitrosylation on C	UNIMOD:275	3
Water Loss on E	UNIMOD:27	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Acetylation on X	UNIMOD:1	2
Ammonia loss on C	UNIMOD:385	2
Asymmetric dimethylarginine on R	UNIMOD:36	2
Deamidated asparagine on N	UNIMOD:7	2
N-acetylglycine on G	UNIMOD:1	2
Phosphothreonine on T	UNIMOD:21	2
Tele-methylhistidine on H	UNIMOD:34	2
4-hydroxyproline on P	UNIMOD:35	1
Carbamyl on K	UNIMOD:5	1
Crotonylation on K	UNIMOD:1363	1
Dimethylated arginine on R	UNIMOD:36	1
Formylation on K	UNIMOD:122	1
Glutarylation on K	UNIMOD:1848	1
HexNAc on S	UNIMOD:43	1
Hydroxybutyrylation on K	—	1
N-acetylthreonine on T	UNIMOD:1	1
N-acetylvaline on V	UNIMOD:1	1
N-myristoyl glycine on G	UNIMOD:45	1
N6-acetyllysine on K	UNIMOD:1	1
N6-biotinyllysine on K	UNIMOD:3	1
N6-succinyllysine on K	—	1
Phosphorylation on Y	UNIMOD:21	1
Succinylation on K	UNIMOD:64	1
Trimethylation on K	UNIMOD:37	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: cfe59305da5a5ecd, written 2026-10-29T09:50:33+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