Generated summary PXD028590 is a DDA label-free dataset (Mus musculus) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 487,235 PSMs, 38,697 peptidoforms and 2,560 protein groups, and the repository holds 34,170 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 487235 where the producer reported 487545 (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
37.50% of protein intensity in the worst file, 16.95% median across 24 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 153878 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6626 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: 1774 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
177 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	487,235
Peptidoforms at 1% FDR	38,697
Protein groups at 1% FDR	2,560
PTM sites	34,170
Quantitative values	610,310
PSMs, all (including decoys and sub-threshold)	1,423,278
MS2 identification rate (pxreprise:DEF-ID-RATE)	39.3%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	20.4%

How it was measured

Organism searched: Mus musculus (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: 24 / 24
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
Pipeline commit: 5aec9eb024d8

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	8,988
Oxidation on M	UNIMOD:35	3,152
Deamidation on N	UNIMOD:7	2,509
Deamidation on Q	UNIMOD:7	2,326
Hydroxylation on P	UNIMOD:35	1,808
Carbamyl on X	UNIMOD:5	1,459
Ammonia loss on N	UNIMOD:385	901
Citrullination on R	UNIMOD:7	771
Ammonia loss on C	UNIMOD:385	717
Hydroxylation on N	UNIMOD:35	455
Hydroxylation on K	UNIMOD:35	370
Carbamyl on M	UNIMOD:5	339
Methylation on K	UNIMOD:34	292
Carbamyl on K	UNIMOD:5	290
Acetylation on K	UNIMOD:1	239
Carbamyl on R	UNIMOD:5	216
Methylation on R	UNIMOD:34	204
N-acetylalanine on A	UNIMOD:1	185
Carboxylation on E	UNIMOD:299	184
Water Loss on E	UNIMOD:27	180
Trimethylation on K	UNIMOD:37	179
4-hydroxyproline on P	UNIMOD:35	175
Phosphorylation on S	UNIMOD:21	166
Carbamyl on C	UNIMOD:5	157
Formylation on K	UNIMOD:122	145
Dimethylation on K	UNIMOD:36	141
Fe[III] on E	UNIMOD:1870	137
Magnesium on E	UNIMOD:956	137
Phosphoserine on S	UNIMOD:21	130
Sodium on E	UNIMOD:30	128
Dimethylation on R	UNIMOD:36	120
Carboxylation on D	UNIMOD:299	112
Fe[II] on E	UNIMOD:952	111
Acetylation on X	UNIMOD:1	104
Phosphorylation on T	UNIMOD:21	92
HexNAc on T	UNIMOD:43	86
Fe[III] on D	UNIMOD:1870	85
HexNAc on S	UNIMOD:43	83
Fe[II] on D	UNIMOD:952	80
Magnesium on D	UNIMOD:956	78
Sodium on D	UNIMOD:30	77
N-acetylmethionine on M	UNIMOD:1	64
N-acetylserine on S	UNIMOD:1	60
Nitrosylation on Y	UNIMOD:354	55
Calcium on E	UNIMOD:951	53
Carboxylation on K	UNIMOD:299	50
Glutarylation on K	UNIMOD:1848	45
Butyrylation on K	UNIMOD:1289	42
GG (Ubiquitination Site) on K	UNIMOD:121	41
Crotonylation on K	UNIMOD:1363	33
Hydroxybutyrylation on K	—	33
N6-acetyllysine on K	UNIMOD:1	31
Phosphorylation on Y	UNIMOD:21	31
Potassium on E	UNIMOD:530	31
Succinylation on K	UNIMOD:64	30
Nitrosylation on C	UNIMOD:275	28
Sulfonation on Y	UNIMOD:40	28
Malonylation on K	UNIMOD:747	26
Calcium on D	UNIMOD:951	25
5-hydroxylysine on K	UNIMOD:35	24
Omega-N-methylarginine on R	UNIMOD:34	22
Potassium on D	UNIMOD:530	22
Asymmetric dimethylarginine on R	UNIMOD:36	21
Phosphothreonine on T	UNIMOD:21	20
N-acetylthreonine on T	UNIMOD:1	16
Cu[I] on E	UNIMOD:531	14
Allysine on K	UNIMOD:352	13
Cu[I] on D	UNIMOD:531	11
N6-methyllysine on K	UNIMOD:34	8
Phosphotyrosine on Y	UNIMOD:21	8
N6,N6,N6-trimethyllysine on K	UNIMOD:37	7
3-hydroxyproline on P	UNIMOD:35	6
N-acetylvaline on V	UNIMOD:1	6
Deamidated asparagine on N	UNIMOD:7	5
N6-succinyllysine on K	—	5
Tele-methylhistidine on H	UNIMOD:34	5
(3R)-3-hydroxyasparagine on N	UNIMOD:35	4
Zinc on D	UNIMOD:954	4
Zinc on E	UNIMOD:954	4
N-acetylcysteine on C	UNIMOD:1	3
N6,N6-dimethyllysine on K	UNIMOD:36	3
S-nitrosocysteine on C	UNIMOD:275	3
4-carboxyglutamate on E	UNIMOD:299	2
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
HexNAc on Nxs	UNIMOD:43	2
N-acetylglycine on G	UNIMOD:1	2
Symmetric dimethylarginine on R	UNIMOD:36	2
(3R)-3-hydroxyaspartate on D	UNIMOD:35	1
2',4',5'-topaquinone on Y	UNIMOD:392	1
4-hydroxylysine on K	UNIMOD:35	1
Cysteine sulfinic acid (-SO2H) on C	UNIMOD:425	1
Dimethylated arginine on R	UNIMOD:36	1
Diphthamide on H	UNIMOD:375	1
HexNAc on Nxt	UNIMOD:43	1
Hydroxyproline on P	UNIMOD:35	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-malonyllysine on K	—	1
S-palmitoyl cysteine on C	UNIMOD:47	1
Sulfocysteine on C	UNIMOD:40	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: 6760c6468208b830, written 2026-10-29T12:39:25+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