Generated summary PXD048720 is a DDA label-free dataset (Rattus norvegicus) with 29 runs, 29 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,325,918 PSMs, 41,818 peptidoforms and 4,202 protein groups, and the repository holds 29,907 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 2 for information

count_mismatch warning
The bundle holds 1.32592e+06 where the producer reported 1.32646e+06 (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 159809 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11691 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: 4658 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.

collapsed_duplicate_rows info
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 5 identifier(s), 7 row(s) dropped, e.g. PXD048720:A0A096MJL4;A0ABK0LV97 written 2 times; quant_values: 145 identifier(s), 203 row(s) dropped, e.g. PXD048720:20220216_105621_Fabio_1_3:label_free:protein_group:PXD048720:A0A096MJL4;A0ABK0LV97:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.

occupancy_decoy_groups info
190 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	1,325,918
Peptidoforms at 1% FDR	41,818
Protein groups at 1% FDR	4,202
PTM sites	29,907
Quantitative values	916,379
PSMs, all (including decoys and sub-threshold)	2,270,193
MS2 identification rate (pxreprise:DEF-ID-RATE)	48.5%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	0.3%

How it was measured

Organism searched: Rattus norvegicus (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: 29 / 29
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000002494_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: 0ba5e4c3fd33

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	10,292
Deamidation on Q	UNIMOD:7	4,432
Deamidation on N	UNIMOD:7	4,193
Oxidation on M	UNIMOD:35	2,408
Citrullination on R	UNIMOD:7	891
Hydroxylation on P	UNIMOD:35	595
Ammonia loss on N	UNIMOD:385	517
Formylation on K	UNIMOD:122	402
Hydroxylation on N	UNIMOD:35	385
Carbamyl on X	UNIMOD:5	355
Carbamyl on M	UNIMOD:5	281
Phosphoserine on S	UNIMOD:21	272
Ammonia loss on C	UNIMOD:385	258
Fe[II] on E	UNIMOD:952	225
Fe[II] on D	UNIMOD:952	208
Methylation on K	UNIMOD:34	203
Fe[III] on E	UNIMOD:1870	200
Acetylation on K	UNIMOD:1	199
Acetylation on X	UNIMOD:1	191
Fe[III] on D	UNIMOD:1870	179
Methylation on R	UNIMOD:34	152
Trimethylation on K	UNIMOD:37	146
N-acetylalanine on A	UNIMOD:1	143
Magnesium on E	UNIMOD:956	137
Water Loss on E	UNIMOD:27	136
Magnesium on D	UNIMOD:956	128
Sodium on E	UNIMOD:30	127
Hydroxylation on K	UNIMOD:35	108
Sodium on D	UNIMOD:30	108
Dimethylation on R	UNIMOD:36	106
Phosphorylation on S	UNIMOD:21	99
Dimethylation on K	UNIMOD:36	97
Calcium on E	UNIMOD:951	80
N-acetylmethionine on M	UNIMOD:1	79
N6-acetyllysine on K	UNIMOD:1	75
Carbamyl on C	UNIMOD:5	71
Carboxylation on E	UNIMOD:299	71
Phosphorylation on T	UNIMOD:21	67
Calcium on D	UNIMOD:951	59
Phosphothreonine on T	UNIMOD:21	59
Carboxylation on D	UNIMOD:299	56
N-acetylserine on S	UNIMOD:1	55
Potassium on D	UNIMOD:530	53
Nitrosylation on C	UNIMOD:275	51
Succinylation on K	UNIMOD:64	50
GG (Ubiquitination Site) on K	UNIMOD:121	42
Potassium on E	UNIMOD:530	39
Sulfonation on Y	UNIMOD:40	35
Carbamyl on R	UNIMOD:5	33
Glutarylation on K	UNIMOD:1848	33
Carbamyl on K	UNIMOD:5	32
Nitrosylation on Y	UNIMOD:354	31
Butyrylation on K	UNIMOD:1289	29
Deamidated asparagine on N	UNIMOD:7	22
HexNAc on T	UNIMOD:43	22
Hydroxybutyrylation on K	—	21
Malonylation on K	UNIMOD:747	20
Omega-N-methylarginine on R	UNIMOD:34	20
Phosphotyrosine on Y	UNIMOD:21	19
N6-succinyllysine on K	—	18
Phosphorylation on Y	UNIMOD:21	18
Carboxylation on K	UNIMOD:299	17
HexNAc on S	UNIMOD:43	15
N6,N6,N6-trimethyllysine on K	UNIMOD:37	15
Asymmetric dimethylarginine on R	UNIMOD:36	12
N-acetylthreonine on T	UNIMOD:1	12
Crotonylation on K	UNIMOD:1363	11
N-acetylvaline on V	UNIMOD:1	8
4-hydroxyproline on P	UNIMOD:35	7
N5-methylglutamine on Q	UNIMOD:34	7
N6-crotonyllysine on K	—	7
ADP-ribosylation on S	UNIMOD:213	6
Pyridoxal phosphate on K	UNIMOD:46	6
Citrulline on R	UNIMOD:7	5
N-acetylglycine on G	UNIMOD:1	5
3'-nitrotyrosine on Y	—	4
N6,N6-dimethyllysine on K	UNIMOD:36	4
N6-glutaryllysine on K	—	4
N6-methyllysine on K	UNIMOD:34	4
Tele-methylhistidine on H	UNIMOD:34	4
Cysteine persulfide on C	UNIMOD:421	3
Dimethylated arginine on R	UNIMOD:36	3
N-acetylcysteine on C	UNIMOD:1	3
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	3
S-nitrosocysteine on C	UNIMOD:275	3
4-carboxyglutamate on E	UNIMOD:299	2
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
5-hydroxylysine on K	UNIMOD:35	2
HexNAc on Nxt	UNIMOD:43	2
Hydroxyproline on P	UNIMOD:35	2
N-myristoyl glycine on G	UNIMOD:45	2
S-farnesyl cysteine on C	UNIMOD:44	2
(3S)-3-hydroxyhistidine on H	—	1
4-hydroxylysine on K	UNIMOD:35	1
Cysteine sulfinic acid (-SO2H) on C	UNIMOD:425	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-biotinyllysine on K	UNIMOD:3	1
N6-isonicotinyllysine on K	UNIMOD:697	1
N6-lipoyllysine on K	UNIMOD:42	1
N6-malonyllysine on K	—	1
S-palmitoyl cysteine on C	UNIMOD:47	1
Symmetric dimethylarginine on R	UNIMOD:36	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: ea1fac3cf3d72f0a, written 2026-10-29T12:16:23+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