Generated summary PXD007906 is a DDA label-free dataset (Homo sapiens) 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 882,422 PSMs, 41,275 peptidoforms and 3,487 protein groups, and the repository holds 26,288 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 882422 where the producer reported 882508 (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 104088 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11555 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: 2113 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: 3 identifier(s), 3 row(s) dropped, e.g. PXD007906:O14782;O15066 written 2 times; quant_values: 72 identifier(s), 72 row(s) dropped, e.g. PXD007906:PSY_NT_CM1_A:label_free:protein_group:PXD007906:O14782;O15066:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.

occupancy_decoy_groups info
153 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	882,422
Peptidoforms at 1% FDR	41,275
Protein groups at 1% FDR	3,487
PTM sites	26,288
Quantitative values	955,353
PSMs, all (including decoys and sub-threshold)	1,076,837
MS2 identification rate (pxreprise:DEF-ID-RATE)	61.1%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	1.0%

How it was measured

Organism searched: Homo sapiens (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: UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
Pipeline commit: 852cea5e1cd7

Modifications

Search engine's name	UNIMOD	Sites
Carbamidomethyl on C	UNIMOD:4	10,028
Deamidation on N	UNIMOD:7	2,734
Deamidation on Q	UNIMOD:7	2,560
Oxidation on M	UNIMOD:35	1,924
Carbamyl on X	UNIMOD:5	1,774
Ammonia loss on N	UNIMOD:385	535
Citrullination on R	UNIMOD:7	451
Hydroxylation on P	UNIMOD:35	405
Fe[II] on E	UNIMOD:952	329
Ammonia loss on C	UNIMOD:385	311
Sodium on E	UNIMOD:30	277
Fe[II] on D	UNIMOD:952	238
N-acetylalanine on A	UNIMOD:1	233
Phosphoserine on S	UNIMOD:21	232
Carbamyl on K	UNIMOD:5	198
Sodium on D	UNIMOD:30	197
Methylation on K	UNIMOD:34	194
Fe[III] on E	UNIMOD:1870	193
Magnesium on E	UNIMOD:956	179
Acetylation on K	UNIMOD:1	152
Hydroxylation on N	UNIMOD:35	144
Fe[III] on D	UNIMOD:1870	133
Magnesium on D	UNIMOD:956	128
Hydroxylation on K	UNIMOD:35	123
Water Loss on E	UNIMOD:27	123
N-acetylmethionine on M	UNIMOD:1	119
Acetylation on X	UNIMOD:1	110
Calcium on E	UNIMOD:951	110
Carbamyl on R	UNIMOD:5	102
Carbamyl on M	UNIMOD:5	86
Dimethylation on K	UNIMOD:36	86
N-acetylserine on S	UNIMOD:1	84
N6-acetyllysine on K	UNIMOD:1	80
Calcium on D	UNIMOD:951	78
Trimethylation on K	UNIMOD:37	72
Carboxylation on E	UNIMOD:299	71
Dimethylation on R	UNIMOD:36	63
Carboxylation on D	UNIMOD:299	58
Potassium on E	UNIMOD:530	57
Carbamyl on C	UNIMOD:5	55
Methylation on R	UNIMOD:34	53
Potassium on D	UNIMOD:530	45
Phosphothreonine on T	UNIMOD:21	43
Phosphorylation on T	UNIMOD:21	42
Phosphorylation on S	UNIMOD:21	40
Formylation on K	UNIMOD:122	39
Omega-N-methylarginine on R	UNIMOD:34	37
HexNAc on T	UNIMOD:43	29
Nitrosylation on C	UNIMOD:275	28
Asymmetric dimethylarginine on R	UNIMOD:36	26
Nitrosylation on Y	UNIMOD:354	26
HexNAc on S	UNIMOD:43	25
Carboxylation on K	UNIMOD:299	23
N-acetylthreonine on T	UNIMOD:1	21
N6-succinyllysine on K	—	21
Sulfonation on Y	UNIMOD:40	19
Hydroxybutyrylation on K	—	18
Butyrylation on K	UNIMOD:1289	17
Malonylation on K	UNIMOD:747	16
Succinylation on K	UNIMOD:64	16
Crotonylation on K	UNIMOD:1363	13
Citrulline on R	UNIMOD:7	12
N6-(2-hydroxyisobutyryl)lysine on K	UNIMOD:1849	12
N6,N6,N6-trimethyllysine on K	UNIMOD:37	11
N6-methyllysine on K	UNIMOD:34	11
4-hydroxyproline on P	UNIMOD:35	10
GG (Ubiquitination Site) on K	UNIMOD:121	10
Glutarylation on K	UNIMOD:1848	10
N-myristoyl glycine on G	UNIMOD:45	10
Dimethylated arginine on R	UNIMOD:36	9
N6,N6-dimethyllysine on K	UNIMOD:36	8
N6-crotonyllysine on K	—	8
N-acetylglycine on G	UNIMOD:1	7
Deamidated asparagine on N	UNIMOD:7	6
Phosphorylation on Y	UNIMOD:21	6
Cu[I] on E	UNIMOD:531	5
S-nitrosocysteine on C	UNIMOD:275	5
N-acetylvaline on V	UNIMOD:1	4
N6-benzoyllysine on K	UNIMOD:136	4
N6-butyryllysine on K	UNIMOD:1289	4
Tele-methylhistidine on H	UNIMOD:34	4
5-glutamyl dopamine on Q	—	3
Cu[I] on D	UNIMOD:531	3
Phosphotyrosine on Y	UNIMOD:21	3
4-carboxyglutamate on E	UNIMOD:299	2
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
N,N,N-trimethylglycine on G	—	2
Zinc on E	UNIMOD:954	2
3'-nitrotyrosine on Y	—	1
4-hydroxylysine on K	UNIMOD:35	1
ADP-ribosylcysteine on C	UNIMOD:213	1
Cysteine persulfide on C	UNIMOD:421	1
Cysteine sulfinic acid (-SO2H) on C	UNIMOD:425	1
Diphthamide on H	UNIMOD:375	1
Hydroxyproline on P	UNIMOD:35	1
N-acetylaspartate on D	UNIMOD:1	1
N-acetylcysteine on C	UNIMOD:1	1
N-acetylglutamate on E	UNIMOD:1	1
N5-methylglutamine on Q	UNIMOD:34	1
N6-isonicotinyllysine on K	UNIMOD:697	1
N6-lipoyllysine on K	UNIMOD:42	1
N6-malonyllysine on K	—	1
N6-methacryllysine on K	—	1
Pros-methylhistidine on H	UNIMOD:34	1
S-(2-succinyl)cysteine on C	UNIMOD:957	1
S-farnesyl cysteine on C	UNIMOD:44	1
Sulfotyrosine on Y	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: 744052f7dfd46f91, written 2026-10-29T09:23:51+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