Generated summary PXD057409 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 484,238 PSMs, 44,770 peptidoforms and 4,053 protein groups, and the repository holds 18,842 PTM sites for it. 4 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, 4 warnings and 1 for information

count_mismatch warning
The bundle holds 484238 where the producer reported 484275 (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.

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 38574 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7388 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: 1663 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
39 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	484,238
Peptidoforms at 1% FDR	44,770
Protein groups at 1% FDR	4,053
PTM sites	18,842
Quantitative values	379,009
PSMs, all (including decoys and sub-threshold)	695,051
MS2 identification rate (pxreprise:DEF-ID-RATE)	79.2%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	0.4%

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: 9 / 9
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	9,592
Deamidation on Q	UNIMOD:7	1,347
Oxidation on M	UNIMOD:35	1,184
Deamidation on N	UNIMOD:7	1,140
Ammonia loss on N	UNIMOD:385	416
Citrullination on R	UNIMOD:7	349
Hydroxylation on P	UNIMOD:35	338
Calcium on E	UNIMOD:951	318
N-acetylalanine on A	UNIMOD:1	294
Calcium on D	UNIMOD:951	290
Sodium on E	UNIMOD:30	254
Ammonia loss on C	UNIMOD:385	250
Acetylation on X	UNIMOD:1	225
Sodium on D	UNIMOD:30	223
N-acetylmethionine on M	UNIMOD:1	158
Magnesium on E	UNIMOD:956	155
Phosphoserine on S	UNIMOD:21	154
Magnesium on D	UNIMOD:956	150
Carbamyl on X	UNIMOD:5	122
Methylation on K	UNIMOD:34	116
Potassium on E	UNIMOD:530	116
N-acetylserine on S	UNIMOD:1	111
Potassium on D	UNIMOD:530	103
Hydroxylation on K	UNIMOD:35	96
Hydroxylation on N	UNIMOD:35	68
Dimethylation on K	UNIMOD:36	63
Phosphorylation on S	UNIMOD:21	59
Acetylation on K	UNIMOD:1	55
N6-acetyllysine on K	UNIMOD:1	52
Water Loss on E	UNIMOD:27	49
GG (Ubiquitination Site) on K	UNIMOD:121	48
Methylation on R	UNIMOD:34	46
Dimethylation on R	UNIMOD:36	42
Malonylation on K	UNIMOD:747	41
Phosphorylation on T	UNIMOD:21	39
Trimethylation on K	UNIMOD:37	33
Carbamyl on M	UNIMOD:5	31
Butyrylation on K	UNIMOD:1289	30
Phosphothreonine on T	UNIMOD:21	30
Glutarylation on K	UNIMOD:1848	29
Succinylation on K	UNIMOD:64	29
Carbamyl on K	UNIMOD:5	27
Crotonylation on K	UNIMOD:1363	27
Hydroxybutyrylation on K	—	26
N-acetylthreonine on T	UNIMOD:1	22
Omega-N-methylarginine on R	UNIMOD:34	22
HexNAc on T	UNIMOD:43	20
Asymmetric dimethylarginine on R	UNIMOD:36	18
Carbamyl on R	UNIMOD:5	16
HexNAc on S	UNIMOD:43	16
N-myristoyl glycine on G	UNIMOD:45	15
Carboxylation on E	UNIMOD:299	14
Fe[II] on D	UNIMOD:952	14
Cu[I] on D	UNIMOD:531	13
Formylation on K	UNIMOD:122	12
N6-succinyllysine on K	—	12
N6-methyllysine on K	UNIMOD:34	11
Sulfonation on Y	UNIMOD:40	11
4-hydroxyproline on P	UNIMOD:35	10
Carboxylation on D	UNIMOD:299	10
Cu[I] on E	UNIMOD:531	10
N6,N6,N6-trimethyllysine on K	UNIMOD:37	10
Nitrosylation on C	UNIMOD:275	9
N-acetylglycine on G	UNIMOD:1	8
N6-glutaryllysine on K	—	8
Phosphotyrosine on Y	UNIMOD:21	8
Carbamyl on C	UNIMOD:5	7
Fe[II] on E	UNIMOD:952	7
N6,N6-dimethyllysine on K	UNIMOD:36	6
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	6
Nitrosylation on Y	UNIMOD:354	6
Phosphorylation on Y	UNIMOD:21	6
Tele-methylhistidine on H	UNIMOD:34	6
Fe[III] on D	UNIMOD:1870	5
Fe[III] on E	UNIMOD:1870	5
N-acetylcysteine on C	UNIMOD:1	5
Pyridoxal phosphate on K	UNIMOD:46	5
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	4
Dimethylated arginine on R	UNIMOD:36	4
N-acetylvaline on V	UNIMOD:1	4
Symmetric dimethylarginine on R	UNIMOD:36	4
N6-crotonyllysine on K	—	3
Zinc on D	UNIMOD:954	3
Zinc on E	UNIMOD:954	3
Carboxylation on K	UNIMOD:299	2
Cysteine persulfide on C	UNIMOD:421	2
Leucine methyl ester on L	UNIMOD:34	2
N5-methylglutamine on Q	UNIMOD:34	2
Pros-methylhistidine on H	UNIMOD:34	2
S-(2-succinyl)cysteine on C	UNIMOD:957	2
S-nitrosocysteine on C	UNIMOD:275	2
S-palmitoyl cysteine on C	UNIMOD:47	2
(3S)-3-hydroxyasparagine on N	—	1
(3S)-3-hydroxylysine on K	—	1
3-hydroxyproline on P	UNIMOD:35	1
4-hydroxylysine on K	UNIMOD:35	1
5-glutamyl serotonin on Q	—	1
5-hydroxylysine on K	UNIMOD:35	1
Cysteine sulfinic acid (-SO2H) on C	UNIMOD:425	1
Diphthamide on H	UNIMOD:375	1
HexNAc on Nxs	UNIMOD:43	1
Hydroxyproline on P	UNIMOD:35	1
N,N,N-trimethylalanine on A	UNIMOD:37	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-biotinyllysine on K	UNIMOD:3	1
N6-isonicotinyllysine on K	UNIMOD:697	1
S-farnesyl cysteine on C	UNIMOD:44	1
Tele-8alpha-FAD histidine on H	UNIMOD:50	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: ede774f706324229, written 2026-10-29T10:53:22+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