Generated summary PXD005014 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 115,772 PSMs, 11,015 peptidoforms and 1,368 protein groups, and the repository holds 4,483 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 115772 where the producer reported 115778 (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 41253 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2400 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: 335 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
93 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	115,772
Peptidoforms at 1% FDR	11,015
Protein groups at 1% FDR	1,368
PTM sites	4,483
Quantitative values	160,919
PSMs, all (including decoys and sub-threshold)	261,010
MS2 identification rate (pxreprise:DEF-ID-RATE)	35.9%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	0.6%

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: 12 / 12
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
Pipeline commit: 089bcc7b11dc

Modifications

Search engine's name	UNIMOD	Sites
Nethylmaleimide on C	UNIMOD:108	1,250
Oxidation on M	UNIMOD:35	475
Deamidation on Q	UNIMOD:7	427
NEM:2H(5) on C	UNIMOD:776	372
Deamidation on N	UNIMOD:7	295
Sodium on E	UNIMOD:30	143
Sodium on D	UNIMOD:30	141
Calcium on D	UNIMOD:951	94
Ammonia loss on N	UNIMOD:385	93
N-acetylalanine on A	UNIMOD:1	92
Hydroxylation on P	UNIMOD:35	75
Nethylmaleimide+water on C	—	74
Calcium on E	UNIMOD:951	72
Magnesium on D	UNIMOD:956	72
Magnesium on E	UNIMOD:956	56
Hydroxylation on N	UNIMOD:35	51
Acetylation on X	UNIMOD:1	42
Hydroxylation on K	UNIMOD:35	34
N-acetylmethionine on M	UNIMOD:1	34
Phosphorylation on S	UNIMOD:21	34
N-acetylserine on S	UNIMOD:1	33
Phosphoserine on S	UNIMOD:21	33
Methylation on K	UNIMOD:34	22
Crotonylation on K	UNIMOD:1363	20
N6-acetyllysine on K	UNIMOD:1	19
Citrullination on R	UNIMOD:7	18
GG (Ubiquitination Site) on K	UNIMOD:121	15
N6-succinyllysine on K	—	14
Phosphorylation on T	UNIMOD:21	14
Butyrylation on K	UNIMOD:1289	12
Carbamyl on X	UNIMOD:5	12
N6,N6,N6-trimethyllysine on K	UNIMOD:37	12
Hydroxybutyrylation on K	—	10
Potassium on D	UNIMOD:530	10
Potassium on E	UNIMOD:530	10
Water Loss on E	UNIMOD:27	10
4-hydroxyproline on P	UNIMOD:35	9
Acetylation on K	UNIMOD:1	9
N-acetylthreonine on T	UNIMOD:1	9
Trimethylation on K	UNIMOD:37	9
Phosphothreonine on T	UNIMOD:21	8
Succinylation on K	UNIMOD:64	8
Dimethylation on K	UNIMOD:36	6
Deamidated asparagine on N	UNIMOD:7	5
Glu to PyroGlu on Q	UNIMOD:28	5
Glutarylation on K	UNIMOD:1848	5
Methylation on R	UNIMOD:34	5
Tele-methylhistidine on H	UNIMOD:34	5
Asymmetric dimethylarginine on R	UNIMOD:36	4
Carbamyl on K	UNIMOD:5	4
Formylation on K	UNIMOD:122	4
N-acetylglycine on G	UNIMOD:1	4
N-myristoyl glycine on G	UNIMOD:45	4
Carboxylation on K	UNIMOD:299	3
HexNAc on T	UNIMOD:43	3
Malonylation on K	UNIMOD:747	3
N-acetylcysteine on C	UNIMOD:1	3
N6,N6-dimethyllysine on K	UNIMOD:36	3
Phosphorylation on Y	UNIMOD:21	3
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Carbamyl on C	UNIMOD:5	2
Carboxylation on E	UNIMOD:299	2
Dimethylation on R	UNIMOD:36	2
HexNAc on S	UNIMOD:43	2
N-acetylvaline on V	UNIMOD:1	2
Symmetric dimethylarginine on R	UNIMOD:36	2
Carbamyl on M	UNIMOD:5	1
Carbamyl on R	UNIMOD:5	1
Carboxylation on D	UNIMOD:299	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-isonicotinyllysine on K	UNIMOD:697	1
N6-malonyllysine on K	—	1
Nitrosylation on C	UNIMOD:275	1
Omega-N-methylarginine on R	UNIMOD:34	1
Sulfonation on Y	UNIMOD:40	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: c4603fc4e4fa267c, written 2026-10-29T09:35:55+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