Generated summary
PXD011740 is a DDA label-free dataset (Homo sapiens) 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 89,011 PSMs, 16,644 peptidoforms and 2,112 protein groups, and the repository holds 6,207 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.
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 2 for information
count_mismatch warning
The bundle holds 89011 where the producer reported 89023 (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 89011 where the producer reported 89023 (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
67.60% of protein intensity in the worst file, 3.01% median across 12 files (DEF-QC-9 v3.5)
67.60% of protein intensity in the worst file, 3.01% median across 12 files (DEF-QC-9 v3.5)
occupancy_not_stored warning
Of 24671 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2195 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 24671 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2195 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: 149 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: 149 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.
unresolved_modifications warning
1 modification(s) could not be mapped to a UNIMOD accession or a mass, and are carried in ProForma as [Info:...] tags: Unimod:Nethylmaleimide+water on C. Their ptm_sites rows exist and carry modification_name, with modification null, so a query by name finds them and a query by UNIMOD accession will not.
1 modification(s) could not be mapped to a UNIMOD accession or a mass, and are carried in ProForma as [Info:...] tags: Unimod:Nethylmaleimide+water on C. Their ptm_sites rows exist and carry modification_name, with modification null, so a query by name finds them and a query by UNIMOD accession will not.
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: 2 identifier(s), 3 row(s) dropped, e.g. PXD011740:A6NGU5;P19440;P36268 written 3 times; quant_values: 29 identifier(s), 41 row(s) dropped, e.g. PXD011740:sample1:label_free:protein_group:PXD011740:A6NGU5;P19440;P36268: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: 2 identifier(s), 3 row(s) dropped, e.g. PXD011740:A6NGU5;P19440;P36268 written 3 times; quant_values: 29 identifier(s), 41 row(s) dropped, e.g. PXD011740:sample1:label_free:protein_group:PXD011740:A6NGU5;P19440;P36268:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
81 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
81 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 | 89,011 |
| Peptidoforms at 1% FDR | 16,644 |
| Protein groups at 1% FDR | 2,112 |
| PTM sites | 6,207 |
| Quantitative values | 131,034 |
| PSMs, all (including decoys and sub-threshold) | 176,667 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 35.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.5% |
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
- 12 / 12
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 766ecc4f6ae7
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 1,406 |
| Nethylmaleimide on C | UNIMOD:108 | 970 |
| NEM:2H(5) on C | UNIMOD:776 | 646 |
| Deamidation on N | UNIMOD:7 | 320 |
| Sodium on E | UNIMOD:30 | 256 |
| Hydroxylation on P | UNIMOD:35 | 233 |
| Oxidation on M | UNIMOD:35 | 229 |
| Deamidation on Q | UNIMOD:7 | 215 |
| Sodium on D | UNIMOD:30 | 195 |
| N-acetylalanine on A | UNIMOD:1 | 179 |
| Nethylmaleimide+water on C | — | 142 |
| Ammonia loss on N | UNIMOD:385 | 127 |
| 4-hydroxyproline on P | UNIMOD:35 | 113 |
| N-acetylmethionine on M | UNIMOD:1 | 84 |
| Magnesium on E | UNIMOD:956 | 72 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 64 |
| N-acetylserine on S | UNIMOD:1 | 63 |
| Magnesium on D | UNIMOD:956 | 61 |
| N6-acetyllysine on K | UNIMOD:1 | 56 |
| Ammonia loss on C | UNIMOD:385 | 49 |
| Calcium on D | UNIMOD:951 | 49 |
| Citrullination on R | UNIMOD:7 | 47 |
| Calcium on E | UNIMOD:951 | 46 |
| Hydroxylation on K | UNIMOD:35 | 40 |
| Glutarylation on K | UNIMOD:1848 | 37 |
| Phosphoserine on S | UNIMOD:21 | 33 |
| Phosphorylation on S | UNIMOD:21 | 24 |
| Nitrosylation on C | UNIMOD:275 | 22 |
| Hydroxylation on N | UNIMOD:35 | 20 |
| N-acetylthreonine on T | UNIMOD:1 | 18 |
| Acetylation on X | UNIMOD:1 | 17 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 16 |
| Methylation on K | UNIMOD:34 | 16 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 15 |
| Nitrosylation on Y | UNIMOD:354 | 15 |
| Acetylation on K | UNIMOD:1 | 13 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 13 |
| Crotonylation on K | UNIMOD:1363 | 12 |
| Carbamyl on X | UNIMOD:5 | 11 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 11 |
| Succinylation on K | UNIMOD:64 | 11 |
| Hydroxyproline on P | UNIMOD:35 | 9 |
| N6-methyllysine on K | UNIMOD:34 | 9 |
| Sulfonation on Y | UNIMOD:40 | 9 |
| Deamidated asparagine on N | UNIMOD:7 | 8 |
| Hydroxybutyrylation on K | — | 8 |
| Phosphothreonine on T | UNIMOD:21 | 8 |
| Potassium on D | UNIMOD:530 | 8 |
| Carbamyl on C | UNIMOD:5 | 6 |
| Omega-N-methylarginine on R | UNIMOD:34 | 6 |
| Phosphorylation on T | UNIMOD:21 | 6 |
| Water Loss on E | UNIMOD:27 | 6 |
| 5-hydroxylysine on K | UNIMOD:35 | 5 |
| Formylation on K | UNIMOD:122 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| Phosphorylation on Y | UNIMOD:21 | 5 |
| Carbamyl on K | UNIMOD:5 | 4 |
| Carbamyl on M | UNIMOD:5 | 4 |
| Dimethylation on R | UNIMOD:36 | 4 |
| Methylation on R | UNIMOD:34 | 4 |
| Potassium on E | UNIMOD:530 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Dimethylation on K | UNIMOD:36 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| HexNAc on S | UNIMOD:43 | 2 |
| N6-glutaryllysine on K | — | 2 |
| N6-succinyllysine on K | — | 2 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Carbamyl on R | UNIMOD:5 | 1 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| Malonylation on K | UNIMOD:747 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-methacryllysine on K | — | 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
b7dbca088aa5c165, written 2026-10-29T09:41:48+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