Generated summary PXD044227 is a DDA label-free dataset (Mus musculus) with 61 runs, 61 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 457,219 PSMs, 29,973 peptidoforms and 4,506 protein groups, and the repository holds 23,252 PTM sites for it. 6 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, 6 warnings and 1 for information

count_mismatch warning
The bundle holds 457219 where the producer reported 457420 (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
4.20% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)

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 310076 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6269 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).

spectral_library warning
mouse's current library moved from version 61 to 62 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD044227\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-14-17-46-26.msp and has NOT been registered, so nothing was lost; merge it deliberately.

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: 584 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
588 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	457,219
Peptidoforms at 1% FDR	29,973
Protein groups at 1% FDR	4,506
PTM sites	23,252
Quantitative values	784,180
PSMs, all (including decoys and sub-threshold)	749,945
MS2 identification rate (pxreprise:DEF-ID-RATE)	18.0%
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: phospho
Instrument vendor: not recorded
Runs / samples: 61 / 61
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 766ecc4f6ae7

Modifications

Search engine's name	UNIMOD	Sites
Phosphoserine on S	UNIMOD:21	5,220
Phosphorylation on S	UNIMOD:21	5,037
Phosphorylation on T	UNIMOD:21	1,679
Oxidation on M	UNIMOD:35	1,383
Carbamidomethyl on C	UNIMOD:4	1,197
Deamidation on N	UNIMOD:7	987
Deamidation on Q	UNIMOD:7	904
Sodium on E	UNIMOD:30	616
Phosphothreonine on T	UNIMOD:21	581
Magnesium on E	UNIMOD:956	554
Magnesium on D	UNIMOD:956	514
Sodium on D	UNIMOD:30	494
Phosphorylation on Y	UNIMOD:21	314
Calcium on D	UNIMOD:951	279
Calcium on E	UNIMOD:951	268
Sulfonation on Y	UNIMOD:40	261
Ammonia loss on N	UNIMOD:385	234
Hydroxylation on P	UNIMOD:35	227
Citrullination on R	UNIMOD:7	171
Fe[III] on E	UNIMOD:1870	138
N-acetylalanine on A	UNIMOD:1	136
Carbamyl on X	UNIMOD:5	123
Hydroxylation on N	UNIMOD:35	109
Potassium on D	UNIMOD:530	104
Fe[III] on D	UNIMOD:1870	101
Phosphotyrosine on Y	UNIMOD:21	101
Acetylation on X	UNIMOD:1	94
Potassium on E	UNIMOD:530	86
Water Loss on E	UNIMOD:27	72
Formylation on K	UNIMOD:122	69
Hydroxylation on K	UNIMOD:35	69
N-acetylserine on S	UNIMOD:1	68
Fe[II] on E	UNIMOD:952	60
N-acetylmethionine on M	UNIMOD:1	58
Fe[II] on D	UNIMOD:952	51
Ammonia loss on C	UNIMOD:385	37
Methylation on K	UNIMOD:34	37
HexNAc on T	UNIMOD:43	35
Acetylation on K	UNIMOD:1	34
HexNAc on S	UNIMOD:43	33
Carboxylation on E	UNIMOD:299	32
Cu[I] on D	UNIMOD:531	26
GG (Ubiquitination Site) on K	UNIMOD:121	26
Cu[I] on E	UNIMOD:531	24
N6-acetyllysine on K	UNIMOD:1	23
Carboxylation on D	UNIMOD:299	20
Carbamyl on K	UNIMOD:5	19
Pyridoxal phosphate on K	UNIMOD:46	19
Glutarylation on K	UNIMOD:1848	18
Nitrosylation on Y	UNIMOD:354	15
Malonylation on K	UNIMOD:747	14
4-hydroxyproline on P	UNIMOD:35	13
Methylation on R	UNIMOD:34	13
N6,N6,N6-trimethyllysine on K	UNIMOD:37	13
Dimethylation on K	UNIMOD:36	12
Trimethylation on K	UNIMOD:37	12
N-myristoyl glycine on G	UNIMOD:45	11
N6-succinyllysine on K	—	11
Omega-N-methylarginine on R	UNIMOD:34	11
Crotonylation on K	UNIMOD:1363	10
Dimethylation on R	UNIMOD:36	10
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	10
N-acetylthreonine on T	UNIMOD:1	9
N6,N6-dimethyllysine on K	UNIMOD:36	9
Carbamyl on R	UNIMOD:5	8
Deamidated asparagine on N	UNIMOD:7	7
N6-methyllysine on K	UNIMOD:34	7
Zinc on D	UNIMOD:954	7
Asymmetric dimethylarginine on R	UNIMOD:36	5
Hydroxybutyrylation on K	—	5
N-acetylglycine on G	UNIMOD:1	5
N-acetylvaline on V	UNIMOD:1	5
N6-glutaryllysine on K	—	5
Succinylation on K	UNIMOD:64	5
ADP-ribosylation on S	UNIMOD:213	4
Carbamyl on M	UNIMOD:5	4
Carboxylation on K	UNIMOD:299	4
HexNAc on Nxt	UNIMOD:43	4
Nitrosylation on C	UNIMOD:275	3
Tele-8alpha-FAD histidine on H	UNIMOD:50	3
Zinc on E	UNIMOD:954	3
Butyrylation on K	UNIMOD:1289	2
N-acetylproline on P	UNIMOD:1	2
N6-malonyllysine on K	—	2
N6-methacryllysine on K	—	2
S-8alpha-FAD cysteine on C	UNIMOD:50	2
Symmetric dimethylarginine on R	UNIMOD:36	2
Tele-methylhistidine on H	UNIMOD:34	2
(3S)-3-hydroxyhistidine on H	—	1
3'-nitrotyrosine on Y	—	1
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	1
Carbamyl on C	UNIMOD:5	1
Citrulline on R	UNIMOD:7	1
Cysteine persulfide on C	UNIMOD:421	1
Deamidated glutamine on Q	UNIMOD:7	1
Diphthamide on H	UNIMOD:375	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N6-(pyridoxal phosphate)lysine on K	UNIMOD:46	1
N6-lipoyllysine on K	UNIMOD:42	1
Pros-8alpha-FAD histidine on H	UNIMOD:50	1
S-farnesyl cysteine on C	UNIMOD:44	1
S-nitrosocysteine on C	UNIMOD:275	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: 21ee092d1c3a2f52, written 2026-10-29T10:44:21+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