Generated summary PXD007188 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 329,746 PSMs, 53,692 peptidoforms and 5,704 protein groups, and the repository holds 27,637 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

count_mismatch warning
The bundle holds 329746 where the producer reported 329768 (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
20.29% of protein intensity in the worst file, 7.04% median across 18 files (DEF-QC-9 v3.5)

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 57768 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 5728 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: 1030 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
57 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	329,746
Peptidoforms at 1% FDR	53,692
Protein groups at 1% FDR	5,704
PTM sites	27,637
Quantitative values	384,552
PSMs, all (including decoys and sub-threshold)	1,134,237
MS2 identification rate (pxreprise:DEF-ID-RATE)	66.6%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	7.6%

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: 18 / 18
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	8,836
Oxidation on M	UNIMOD:35	3,804
Deamidation on N	UNIMOD:7	2,388
Deamidation on Q	UNIMOD:7	1,628
Carbamyl on X	UNIMOD:5	725
Formylation on K	UNIMOD:122	629
Hydroxylation on P	UNIMOD:35	590
Ammonia loss on N	UNIMOD:385	453
Carbamyl on M	UNIMOD:5	417
Sodium on E	UNIMOD:30	402
Acetylation on K	UNIMOD:1	393
Phosphoserine on S	UNIMOD:21	375
N-acetylalanine on A	UNIMOD:1	366
Citrullination on R	UNIMOD:7	338
Magnesium on E	UNIMOD:956	321
Sodium on D	UNIMOD:30	294
Methylation on K	UNIMOD:34	284
Ammonia loss on C	UNIMOD:385	239
Hydroxylation on N	UNIMOD:35	216
Magnesium on D	UNIMOD:956	212
Acetylation on X	UNIMOD:1	165
Hydroxylation on K	UNIMOD:35	143
N-acetylmethionine on M	UNIMOD:1	138
Methylation on R	UNIMOD:34	133
N-acetylserine on S	UNIMOD:1	131
Calcium on E	UNIMOD:951	115
Trimethylation on K	UNIMOD:37	114
Dimethylation on K	UNIMOD:36	113
N6-acetyllysine on K	UNIMOD:1	112
Phosphorylation on S	UNIMOD:21	112
Calcium on D	UNIMOD:951	108
Water Loss on E	UNIMOD:27	83
Carboxylation on D	UNIMOD:299	81
Dimethylation on R	UNIMOD:36	80
Phosphorylation on T	UNIMOD:21	75
Carbamyl on K	UNIMOD:5	73
Carboxylation on E	UNIMOD:299	73
Fe[II] on E	UNIMOD:952	61
Glutarylation on K	UNIMOD:1848	59
Omega-N-methylarginine on R	UNIMOD:34	58
Fe[III] on E	UNIMOD:1870	57
GG (Ubiquitination Site) on K	UNIMOD:121	56
Phosphothreonine on T	UNIMOD:21	56
Crotonylation on K	UNIMOD:1363	48
Fe[III] on D	UNIMOD:1870	47
HexNAc on S	UNIMOD:43	44
Asymmetric dimethylarginine on R	UNIMOD:36	43
Malonylation on K	UNIMOD:747	43
Potassium on D	UNIMOD:530	40
Nitrosylation on Y	UNIMOD:354	37
Carbamyl on C	UNIMOD:5	35
HexNAc on T	UNIMOD:43	35
Butyrylation on K	UNIMOD:1289	33
Potassium on E	UNIMOD:530	33
Fe[II] on D	UNIMOD:952	31
Hydroxybutyrylation on K	—	30
Nitrosylation on C	UNIMOD:275	30
Carbamyl on R	UNIMOD:5	29
N-acetylthreonine on T	UNIMOD:1	29
Succinylation on K	UNIMOD:64	26
N6-methyllysine on K	UNIMOD:34	23
Cu[I] on E	UNIMOD:531	22
4-hydroxyproline on P	UNIMOD:35	19
N6,N6-dimethyllysine on K	UNIMOD:36	19
N6,N6,N6-trimethyllysine on K	UNIMOD:37	17
Phosphotyrosine on Y	UNIMOD:21	16
Carboxylation on K	UNIMOD:299	15
Phosphorylation on Y	UNIMOD:21	15
Cu[I] on D	UNIMOD:531	14
Deamidated asparagine on N	UNIMOD:7	13
Sulfonation on Y	UNIMOD:40	12
N6-succinyllysine on K	—	11
N-myristoyl glycine on G	UNIMOD:45	10
Dimethylated arginine on R	UNIMOD:36	9
Pyridoxal phosphate on K	UNIMOD:46	9
Hydroxyproline on P	UNIMOD:35	8
ADP-ribosylation on S	UNIMOD:213	7
N-acetylglycine on G	UNIMOD:1	7
Zinc on D	UNIMOD:954	7
Zinc on E	UNIMOD:954	5
N-acetylvaline on V	UNIMOD:1	4
N6-glutaryllysine on K	—	4
Tele-methylhistidine on H	UNIMOD:34	4
N-acetylcysteine on C	UNIMOD:1	3
N5-methylglutamine on Q	UNIMOD:34	3
N6-crotonyllysine on K	—	3
Pros-methylhistidine on H	UNIMOD:34	3
S-nitrosocysteine on C	UNIMOD:275	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Citrulline on R	UNIMOD:7	2
Cysteine sulfonic acid (-SO3H) on C	UNIMOD:345	2
N-acetylproline on P	UNIMOD:1	2
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	2
N6-methacryllysine on K	—	2
S-farnesyl cysteine on C	UNIMOD:44	2
(3S)-3-hydroxyhistidine on H	—	1
(3S)-3-hydroxylysine on K	—	1
3'-nitrotyrosine on Y	—	1
4-hydroxylysine on K	UNIMOD:35	1
Cysteine persulfide on C	UNIMOD:421	1
Cysteine sulfinic acid (-SO2H) on C	UNIMOD:425	1
Diphthamide on H	UNIMOD:375	1
HexNAc on Nxt	UNIMOD:43	1
Hypusine on K	UNIMOD:379	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-benzoyllysine on K	UNIMOD:136	1
N6-isonicotinyllysine on K	UNIMOD:697	1
S-(2-succinyl)cysteine on C	UNIMOD:957	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: 18f11a83f74ce171, written 2026-10-29T10:19:19+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