Generated summary
PXD008934 is a DDA label-free dataset (Homo sapiens) with 34 runs, 34 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,832,742 PSMs, 71,950 peptidoforms and 4,532 protein groups, and the repository holds 66,232 PTM sites for it. 3 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, 3 warnings and 2 for information
count_mismatch warning
The bundle holds 1.83274e+06 where the producer reported 1.83404e+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.
The bundle holds 1.83274e+06 where the producer reported 1.83404e+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.
occupancy_not_stored warning
Of 348994 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 102 duplicate entry for one site and run (identical values; same protein group); 14608 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 348994 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 102 duplicate entry for one site and run (identical values; same protein group); 14608 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: 9412 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: 9412 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: 8 identifier(s), 13 row(s) dropped, e.g. PXD008934:A6NM11;A6NMS7 written 2 times; quant_values: 272 identifier(s), 442 row(s) dropped, e.g. PXD008934:Prosser_1004:label_free:protein_group:PXD008934:A6NM11;A6NMS7:QuantProject:DEF-PROT-SPC written 2 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: 8 identifier(s), 13 row(s) dropped, e.g. PXD008934:A6NM11;A6NMS7 written 2 times; quant_values: 272 identifier(s), 442 row(s) dropped, e.g. PXD008934:Prosser_1004:label_free:protein_group:PXD008934:A6NM11;A6NMS7:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
355 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
355 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 | 1,832,742 |
| Peptidoforms at 1% FDR | 71,950 |
| Protein groups at 1% FDR | 4,532 |
| PTM sites | 66,232 |
| Quantitative values | 1,237,470 |
| PSMs, all (including decoys and sub-threshold) | 3,698,941 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 61.0% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.2% |
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
- Thermo
- Runs / samples
- 34 / 34
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 813e3bf1d29a
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 13,544 |
| Deamidation on Q | UNIMOD:7 | 7,227 |
| Carbamyl on X | UNIMOD:5 | 7,096 |
| Deamidation on N | UNIMOD:7 | 7,000 |
| Oxidation on M | UNIMOD:35 | 5,360 |
| Citrullination on R | UNIMOD:7 | 2,458 |
| Carbamyl on K | UNIMOD:5 | 1,795 |
| Hydroxylation on P | UNIMOD:35 | 1,636 |
| Carbamyl on M | UNIMOD:5 | 1,216 |
| Acetylation on K | UNIMOD:1 | 1,138 |
| Methylation on K | UNIMOD:34 | 902 |
| Hydroxylation on N | UNIMOD:35 | 797 |
| Sodium on E | UNIMOD:30 | 696 |
| Carboxylation on E | UNIMOD:299 | 695 |
| Ammonia loss on N | UNIMOD:385 | 688 |
| Trimethylation on K | UNIMOD:37 | 653 |
| Carboxylation on D | UNIMOD:299 | 607 |
| Carbamyl on R | UNIMOD:5 | 587 |
| Sodium on D | UNIMOD:30 | 556 |
| Phosphoserine on S | UNIMOD:21 | 529 |
| Magnesium on E | UNIMOD:956 | 450 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 443 |
| Hydroxylation on K | UNIMOD:35 | 432 |
| Methylation on R | UNIMOD:34 | 432 |
| Formylation on K | UNIMOD:122 | 399 |
| Dimethylation on K | UNIMOD:36 | 388 |
| Fe[III] on E | UNIMOD:1870 | 386 |
| Magnesium on D | UNIMOD:956 | 381 |
| Carbamyl on C | UNIMOD:5 | 362 |
| N6-acetyllysine on K | UNIMOD:1 | 354 |
| Fe[II] on E | UNIMOD:952 | 342 |
| Glutarylation on K | UNIMOD:1848 | 318 |
| Fe[II] on D | UNIMOD:952 | 310 |
| Fe[III] on D | UNIMOD:1870 | 303 |
| Calcium on E | UNIMOD:951 | 297 |
| Carboxylation on K | UNIMOD:299 | 285 |
| N-acetylalanine on A | UNIMOD:1 | 266 |
| Calcium on D | UNIMOD:951 | 239 |
| Nitrosylation on Y | UNIMOD:354 | 227 |
| Ammonia loss on C | UNIMOD:385 | 225 |
| Dimethylation on R | UNIMOD:36 | 218 |
| Succinylation on K | UNIMOD:64 | 210 |
| Hydroxybutyrylation on K | — | 185 |
| Potassium on E | UNIMOD:530 | 185 |
| Potassium on D | UNIMOD:530 | 166 |
| Water Loss on E | UNIMOD:27 | 147 |
| N6-succinyllysine on K | — | 125 |
| Acetylation on X | UNIMOD:1 | 122 |
| Phosphothreonine on T | UNIMOD:21 | 120 |
| Nitrosylation on C | UNIMOD:275 | 115 |
| Phosphorylation on S | UNIMOD:21 | 115 |
| Malonylation on K | UNIMOD:747 | 114 |
| 4-hydroxyproline on P | UNIMOD:35 | 112 |
| N-acetylserine on S | UNIMOD:1 | 108 |
| Phosphorylation on T | UNIMOD:21 | 104 |
| N-acetylmethionine on M | UNIMOD:1 | 102 |
| Butyrylation on K | UNIMOD:1289 | 101 |
| HexNAc on T | UNIMOD:43 | 72 |
| Crotonylation on K | UNIMOD:1363 | 70 |
| HexNAc on S | UNIMOD:43 | 67 |
| Cu[I] on D | UNIMOD:531 | 49 |
| Cu[I] on E | UNIMOD:531 | 41 |
| Omega-N-methylarginine on R | UNIMOD:34 | 41 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 31 |
| Pyridoxal phosphate on K | UNIMOD:46 | 26 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 25 |
| N-acetylthreonine on T | UNIMOD:1 | 24 |
| N6-methyllysine on K | UNIMOD:34 | 23 |
| Sulfonation on Y | UNIMOD:40 | 23 |
| Phosphorylation on Y | UNIMOD:21 | 22 |
| Phosphotyrosine on Y | UNIMOD:21 | 21 |
| Deamidated asparagine on N | UNIMOD:7 | 18 |
| Zinc on D | UNIMOD:954 | 16 |
| N-myristoyl glycine on G | UNIMOD:45 | 14 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 13 |
| Zinc on E | UNIMOD:954 | 13 |
| Hydroxyproline on P | UNIMOD:35 | 12 |
| N-acetylglycine on G | UNIMOD:1 | 8 |
| N-acetylvaline on V | UNIMOD:1 | 8 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 8 |
| 5-hydroxylysine on K | UNIMOD:35 | 7 |
| Dimethylated arginine on R | UNIMOD:36 | 7 |
| N5-methylglutamine on Q | UNIMOD:34 | 6 |
| N6-malonyllysine on K | — | 6 |
| N6-methacryllysine on K | — | 6 |
| S-nitrosocysteine on C | UNIMOD:275 | 6 |
| 3'-nitrotyrosine on Y | — | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Citrulline on R | UNIMOD:7 | 4 |
| N6-benzoyllysine on K | UNIMOD:136 | 4 |
| N6-butyryllysine on K | UNIMOD:1289 | 3 |
| 3-oxoalanine (Cys) on C | UNIMOD:402 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| HexNAc on Nxt | UNIMOD:43 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| N6-glutaryllysine on K | — | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Allysine on K | UNIMOD:352 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 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 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N-pyruvate 2-iminyl-valine on V | UNIMOD:422 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| Phosphohistidine on H | UNIMOD:21 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 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
1a400620c1bb4e90, written 2026-10-29T12:21:47+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