Generated summary
PXD069093 is a DDA label-free dataset (Homo sapiens) with 16 runs, 16 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 490,676 PSMs, 22,902 peptidoforms and 2,078 protein groups, and the repository holds 15,824 PTM sites for it. 5 open warnings about it are recorded.
Written from catalog fields only (D17), with no model involved. It says nothing the tables below do not.
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, 5 warnings and 2 for information
count_mismatch warning
The bundle holds 490676 where the producer reported 490711 (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.
The bundle holds 490676 where the producer reported 490711 (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.
high_contamination warning
10.42% of protein intensity in the worst file, 5.86% median across 16 files (DEF-QC-9 v3.5)
10.42% of protein intensity in the worst file, 5.86% median across 16 files (DEF-QC-9 v3.5)
occupancy_not_stored warning
Of 85366 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3272 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).
Of 85366 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3272 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).
sdrf_skeleton warning
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
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: 1657 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.
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: 1657 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), 4 row(s) dropped, e.g. PXD069093:A6NDE4;A6NEQ0;P0C7P1;P0DJD3;P0DJD4;Q15415 written 3 times; quant_values: 48 identifier(s), 64 row(s) dropped, e.g. PXD069093:200928-Pollok-Palbo-05:label_free:protein_group:PXD069093:A6NDE4;A6NEQ0;P0C7P1;P0DJD3;P0DJD4;Q15415:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
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), 4 row(s) dropped, e.g. PXD069093:A6NDE4;A6NEQ0;P0C7P1;P0DJD3;P0DJD4;Q15415 written 3 times; quant_values: 48 identifier(s), 64 row(s) dropped, e.g. PXD069093:200928-Pollok-Palbo-05:label_free:protein_group:PXD069093:A6NDE4;A6NEQ0;P0C7P1;P0DJD3;P0DJD4;Q15415:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
130 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
130 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 | 490,676 |
| Peptidoforms at 1% FDR | 22,902 |
| Protein groups at 1% FDR | 2,078 |
| PTM sites | 15,824 |
| Quantitative values | 318,398 |
| PSMs, all (including decoys and sub-threshold) | 1,250,898 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 34.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 4.8% |
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
- affinity_purification
- Instrument vendor
- Thermo
- Runs / samples
- 16 / 16
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 2,404 |
| Carbamidomethyl on C | UNIMOD:4 | 1,889 |
| Deamidation on Q | UNIMOD:7 | 1,707 |
| Deamidation on N | UNIMOD:7 | 1,295 |
| Hydroxylation on P | UNIMOD:35 | 621 |
| Citrullination on R | UNIMOD:7 | 340 |
| Magnesium on E | UNIMOD:956 | 317 |
| Ammonia loss on N | UNIMOD:385 | 315 |
| Calcium on E | UNIMOD:951 | 313 |
| Sodium on E | UNIMOD:30 | 279 |
| Fe[II] on E | UNIMOD:952 | 240 |
| Hydroxylation on N | UNIMOD:35 | 237 |
| Calcium on D | UNIMOD:951 | 227 |
| Magnesium on D | UNIMOD:956 | 214 |
| Sodium on D | UNIMOD:30 | 190 |
| Potassium on E | UNIMOD:530 | 173 |
| Fe[II] on D | UNIMOD:952 | 155 |
| Hydroxylation on K | UNIMOD:35 | 148 |
| 4-hydroxyproline on P | UNIMOD:35 | 135 |
| Acetylation on K | UNIMOD:1 | 129 |
| Cu[I] on E | UNIMOD:531 | 127 |
| Fe[III] on E | UNIMOD:1870 | 125 |
| Potassium on D | UNIMOD:530 | 111 |
| Carbamyl on X | UNIMOD:5 | 107 |
| Carboxylation on E | UNIMOD:299 | 105 |
| N-acetylalanine on A | UNIMOD:1 | 97 |
| Methylation on K | UNIMOD:34 | 93 |
| Water Loss on E | UNIMOD:27 | 86 |
| Phosphoserine on S | UNIMOD:21 | 81 |
| Fe[III] on D | UNIMOD:1870 | 76 |
| Zinc on E | UNIMOD:954 | 72 |
| Cu[I] on D | UNIMOD:531 | 71 |
| Methylation on R | UNIMOD:34 | 58 |
| N-acetylmethionine on M | UNIMOD:1 | 56 |
| Phosphorylation on S | UNIMOD:21 | 50 |
| Zinc on D | UNIMOD:954 | 48 |
| Formylation on K | UNIMOD:122 | 46 |
| N-acetylserine on S | UNIMOD:1 | 44 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 43 |
| Carboxylation on D | UNIMOD:299 | 40 |
| Acetylation on X | UNIMOD:1 | 36 |
| Phosphorylation on T | UNIMOD:21 | 36 |
| Dimethylation on R | UNIMOD:36 | 33 |
| Omega-N-methylarginine on R | UNIMOD:34 | 30 |
| Nitrosylation on Y | UNIMOD:354 | 29 |
| Dimethylation on K | UNIMOD:36 | 28 |
| N6-acetyllysine on K | UNIMOD:1 | 28 |
| Carbamyl on K | UNIMOD:5 | 23 |
| Phosphothreonine on T | UNIMOD:21 | 20 |
| Carboxylation on K | UNIMOD:299 | 19 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 12 |
| Carbamyl on M | UNIMOD:5 | 11 |
| Glutarylation on K | UNIMOD:1848 | 11 |
| Malonylation on K | UNIMOD:747 | 11 |
| Ammonia loss on C | UNIMOD:385 | 10 |
| Trimethylation on K | UNIMOD:37 | 10 |
| 5-hydroxylysine on K | UNIMOD:35 | 9 |
| N-acetylthreonine on T | UNIMOD:1 | 9 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 9 |
| Phosphotyrosine on Y | UNIMOD:21 | 9 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 8 |
| HexNAc on S | UNIMOD:43 | 8 |
| HexNAc on T | UNIMOD:43 | 8 |
| Sulfonation on Y | UNIMOD:40 | 8 |
| Crotonylation on K | UNIMOD:1363 | 7 |
| Dimethylated arginine on R | UNIMOD:36 | 7 |
| Phosphorylation on Y | UNIMOD:21 | 7 |
| Nitrosylation on C | UNIMOD:275 | 6 |
| Deamidated asparagine on N | UNIMOD:7 | 5 |
| Hydroxybutyrylation on K | — | 5 |
| N6-methyllysine on K | UNIMOD:34 | 5 |
| Carbamyl on R | UNIMOD:5 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| N6-succinyllysine on K | — | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| HexNAc on Nxs | UNIMOD:43 | 3 |
| Hydroxyproline on P | UNIMOD:35 | 3 |
| Succinylation on K | UNIMOD:64 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Allysine on K | UNIMOD:352 | 2 |
| Carbamyl on C | UNIMOD:5 | 2 |
| N6-benzoyllysine on K | UNIMOD:136 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylglycine on G | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-glutaryllysine on K | — | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 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
6c4685f0e4bdebfa, written 2026-10-29T09:58:12+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