Generated summary
PXD008050 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 937,570 PSMs, 63,990 peptidoforms and 5,614 protein groups, and the repository holds 40,949 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 937570 where the producer reported 937636 (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 937570 where the producer reported 937636 (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 172076 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 144 duplicate entry for one site and run (identical values; same protein group); 10386 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 172076 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 144 duplicate entry for one site and run (identical values; same protein group); 10386 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: 4374 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: 4374 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), 2 row(s) dropped, e.g. PXD008050:P01241;P01242;P0DML2;P0DML3 written 2 times; quant_values: 54 identifier(s), 54 row(s) dropped, e.g. PXD008050:EC06-HTkCtrl-BA1-P1144-1:label_free:protein_group:PXD008050:P01241;P01242;P0DML2;P0DML3:QuantProject:DEF-PROT-INT 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: 2 identifier(s), 2 row(s) dropped, e.g. PXD008050:P01241;P01242;P0DML2;P0DML3 written 2 times; quant_values: 54 identifier(s), 54 row(s) dropped, e.g. PXD008050:EC06-HTkCtrl-BA1-P1144-1:label_free:protein_group:PXD008050:P01241;P01242;P0DML2;P0DML3:QuantProject:DEF-PROT-INT written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
86 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
86 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 | 937,570 |
| Peptidoforms at 1% FDR | 63,990 |
| Protein groups at 1% FDR | 5,614 |
| PTM sites | 40,949 |
| Quantitative values | 966,530 |
| PSMs, all (including decoys and sub-threshold) | 1,526,262 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 60.7% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.4% |
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
- 18 / 18
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 9df4ce025f23
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 14,550 |
| Deamidation on N | UNIMOD:7 | 5,318 |
| Deamidation on Q | UNIMOD:7 | 5,060 |
| Oxidation on M | UNIMOD:35 | 2,679 |
| Citrullination on R | UNIMOD:7 | 1,081 |
| Carbamyl on X | UNIMOD:5 | 1,031 |
| Ammonia loss on N | UNIMOD:385 | 800 |
| Carbamyl on K | UNIMOD:5 | 688 |
| Ammonia loss on C | UNIMOD:385 | 675 |
| Hydroxylation on P | UNIMOD:35 | 463 |
| Phosphoserine on S | UNIMOD:21 | 331 |
| N-acetylalanine on A | UNIMOD:1 | 325 |
| Fe[III] on E | UNIMOD:1870 | 320 |
| Fe[III] on D | UNIMOD:1870 | 265 |
| Hydroxylation on N | UNIMOD:35 | 252 |
| N-acetylmethionine on M | UNIMOD:1 | 185 |
| Fe[II] on E | UNIMOD:952 | 181 |
| Phosphorylation on S | UNIMOD:21 | 175 |
| Fe[II] on D | UNIMOD:952 | 168 |
| Methylation on K | UNIMOD:34 | 166 |
| Sodium on E | UNIMOD:30 | 166 |
| Sodium on D | UNIMOD:30 | 162 |
| Hydroxylation on K | UNIMOD:35 | 156 |
| Magnesium on E | UNIMOD:956 | 153 |
| Acetylation on X | UNIMOD:1 | 144 |
| Acetylation on K | UNIMOD:1 | 138 |
| N6-acetyllysine on K | UNIMOD:1 | 137 |
| Carbamyl on M | UNIMOD:5 | 130 |
| Formylation on K | UNIMOD:122 | 130 |
| Magnesium on D | UNIMOD:956 | 127 |
| N-acetylserine on S | UNIMOD:1 | 121 |
| Methylation on R | UNIMOD:34 | 97 |
| Water Loss on E | UNIMOD:27 | 94 |
| Dimethylation on K | UNIMOD:36 | 79 |
| Phosphorylation on T | UNIMOD:21 | 69 |
| Carbamyl on R | UNIMOD:5 | 65 |
| Carboxylation on K | UNIMOD:299 | 55 |
| HexNAc on S | UNIMOD:43 | 54 |
| Omega-N-methylarginine on R | UNIMOD:34 | 52 |
| Dimethylation on R | UNIMOD:36 | 50 |
| Phosphothreonine on T | UNIMOD:21 | 49 |
| Carboxylation on D | UNIMOD:299 | 47 |
| Carboxylation on E | UNIMOD:299 | 46 |
| N6-methyllysine on K | UNIMOD:34 | 46 |
| Calcium on D | UNIMOD:951 | 43 |
| Calcium on E | UNIMOD:951 | 42 |
| Trimethylation on K | UNIMOD:37 | 42 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 41 |
| Potassium on E | UNIMOD:530 | 39 |
| HexNAc on T | UNIMOD:43 | 37 |
| Nitrosylation on Y | UNIMOD:354 | 34 |
| Carbamyl on C | UNIMOD:5 | 28 |
| N-acetylthreonine on T | UNIMOD:1 | 27 |
| Phosphorylation on Y | UNIMOD:21 | 27 |
| Potassium on D | UNIMOD:530 | 27 |
| Malonylation on K | UNIMOD:747 | 26 |
| Sulfonation on Y | UNIMOD:40 | 26 |
| Glutarylation on K | UNIMOD:1848 | 25 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 25 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 23 |
| Nitrosylation on C | UNIMOD:275 | 22 |
| N6-glutaryllysine on K | — | 20 |
| 4-hydroxyproline on P | UNIMOD:35 | 19 |
| Butyrylation on K | UNIMOD:1289 | 19 |
| Deamidated asparagine on N | UNIMOD:7 | 19 |
| N6-succinyllysine on K | — | 18 |
| Succinylation on K | UNIMOD:64 | 18 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 15 |
| Crotonylation on K | UNIMOD:1363 | 11 |
| Cu[I] on E | UNIMOD:531 | 11 |
| Cu[I] on D | UNIMOD:531 | 10 |
| Phosphotyrosine on Y | UNIMOD:21 | 10 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 9 |
| Dimethylated arginine on R | UNIMOD:36 | 8 |
| Hydroxybutyrylation on K | — | 8 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| N6-benzoyllysine on K | UNIMOD:136 | 6 |
| 5-glutamyl dopamine on Q | — | 5 |
| N5-methylglutamine on Q | UNIMOD:34 | 5 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 5 |
| N6-butyryllysine on K | UNIMOD:1289 | 5 |
| N6-methacryllysine on K | — | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| S-nitrosocysteine on C | UNIMOD:275 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| N6-propionyllysine on K | UNIMOD:58 | 3 |
| Pyridoxal phosphate on K | UNIMOD:46 | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-crotonyllysine on K | — | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| Zinc on E | UNIMOD:954 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-malonyllysine on K | — | 1 |
| S-(15-deoxy-Delta12,14-prostaglandin J2-9-yl)cysteine on C | — | 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
92b316ca74569432, written 2026-10-29T12:36:01+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