Generated summary
PXD026219 is a DDA label-free dataset (Homo sapiens) with 41 runs, 41 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 632,869 PSMs, 24,889 peptidoforms and 2,555 protein groups, and the repository holds 21,985 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.
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 632869 where the producer reported 633013 (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 632869 where the producer reported 633013 (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.
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 107779 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2984 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 107779 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2984 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: 8983 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: 8983 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: 2 identifier(s), 3 row(s) dropped, e.g. PXD026219:A6NMD2;D6RF30;H3BQL2 written 3 times; quant_values: 82 identifier(s), 123 row(s) dropped, e.g. PXD026219:180606_Cesare_1AM_1_1:label_free:protein_group:PXD026219:A6NMD2;D6RF30;H3BQL2: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. PXD026219:A6NMD2;D6RF30;H3BQL2 written 3 times; quant_values: 82 identifier(s), 123 row(s) dropped, e.g. PXD026219:180606_Cesare_1AM_1_1:label_free:protein_group:PXD026219:A6NMD2;D6RF30;H3BQL2:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
128 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
128 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 | 632,869 |
| Peptidoforms at 1% FDR | 24,889 |
| Protein groups at 1% FDR | 2,555 |
| PTM sites | 21,985 |
| Quantitative values | 970,814 |
| PSMs, all (including decoys and sub-threshold) | 908,453 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 33.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.1% |
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
- 41 / 41
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0ba5e4c3fd33
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 6,416 |
| Carbamyl on X | UNIMOD:5 | 2,887 |
| Oxidation on M | UNIMOD:35 | 2,805 |
| Deamidation on Q | UNIMOD:7 | 1,751 |
| Deamidation on N | UNIMOD:7 | 1,568 |
| Hydroxylation on P | UNIMOD:35 | 652 |
| Carbamyl on K | UNIMOD:5 | 442 |
| Hydroxylation on N | UNIMOD:35 | 371 |
| Ammonia loss on N | UNIMOD:385 | 365 |
| Citrullination on R | UNIMOD:7 | 324 |
| Hydroxylation on K | UNIMOD:35 | 247 |
| Phosphoserine on S | UNIMOD:21 | 211 |
| Sodium on E | UNIMOD:30 | 201 |
| Carbamyl on M | UNIMOD:5 | 191 |
| Methylation on K | UNIMOD:34 | 172 |
| Fe[III] on E | UNIMOD:1870 | 167 |
| Carbamyl on R | UNIMOD:5 | 152 |
| Phosphorylation on S | UNIMOD:21 | 149 |
| Acetylation on K | UNIMOD:1 | 140 |
| Ammonia loss on C | UNIMOD:385 | 136 |
| N6-acetyllysine on K | UNIMOD:1 | 128 |
| Calcium on E | UNIMOD:951 | 118 |
| Carboxylation on E | UNIMOD:299 | 117 |
| Phosphorylation on T | UNIMOD:21 | 111 |
| Magnesium on E | UNIMOD:956 | 110 |
| 4-hydroxyproline on P | UNIMOD:35 | 107 |
| Calcium on D | UNIMOD:951 | 103 |
| Dimethylation on K | UNIMOD:36 | 102 |
| Water Loss on E | UNIMOD:27 | 102 |
| Sodium on D | UNIMOD:30 | 96 |
| Fe[II] on E | UNIMOD:952 | 83 |
| Fe[III] on D | UNIMOD:1870 | 76 |
| Magnesium on D | UNIMOD:956 | 71 |
| Carboxylation on D | UNIMOD:299 | 70 |
| Nitrosylation on Y | UNIMOD:354 | 64 |
| Potassium on E | UNIMOD:530 | 63 |
| Methylation on R | UNIMOD:34 | 61 |
| Fe[II] on D | UNIMOD:952 | 56 |
| N-acetylalanine on A | UNIMOD:1 | 53 |
| Dimethylation on R | UNIMOD:36 | 50 |
| Potassium on D | UNIMOD:530 | 49 |
| Phosphothreonine on T | UNIMOD:21 | 41 |
| Carbamyl on C | UNIMOD:5 | 40 |
| Sulfonation on Y | UNIMOD:40 | 37 |
| Phosphorylation on Y | UNIMOD:21 | 32 |
| Trimethylation on K | UNIMOD:37 | 32 |
| Acetylation on X | UNIMOD:1 | 31 |
| N-acetylserine on S | UNIMOD:1 | 31 |
| Formylation on K | UNIMOD:122 | 27 |
| Omega-N-methylarginine on R | UNIMOD:34 | 24 |
| Carboxylation on K | UNIMOD:299 | 23 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 21 |
| N-acetylmethionine on M | UNIMOD:1 | 20 |
| HexNAc on T | UNIMOD:43 | 18 |
| N6-methyllysine on K | UNIMOD:34 | 17 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 15 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 15 |
| Phosphotyrosine on Y | UNIMOD:21 | 15 |
| Glutarylation on K | UNIMOD:1848 | 14 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 13 |
| N6-succinyllysine on K | — | 12 |
| HexNAc on S | UNIMOD:43 | 11 |
| Deamidated asparagine on N | UNIMOD:7 | 10 |
| Malonylation on K | UNIMOD:747 | 10 |
| Cu[I] on D | UNIMOD:531 | 9 |
| Hydroxybutyrylation on K | — | 9 |
| Cu[I] on E | UNIMOD:531 | 8 |
| Nitrosylation on C | UNIMOD:275 | 8 |
| Succinylation on K | UNIMOD:64 | 8 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 7 |
| Pyridoxal phosphate on K | UNIMOD:46 | 7 |
| N-acetylthreonine on T | UNIMOD:1 | 6 |
| Butyrylation on K | UNIMOD:1289 | 5 |
| Pros-methylhistidine on H | UNIMOD:34 | 5 |
| Crotonylation on K | UNIMOD:1363 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| N,N,N-trimethylglycine on G | — | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| (3S)-3-hydroxyasparagine on N | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-methacryllysine on K | — | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 1 |
| Zinc on E | UNIMOD:954 | 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
3a567692da5260f1, written 2026-10-29T10:42:12+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