Generated summary
PXD017475 is a DDA label-free dataset (Homo sapiens) with 19 runs, 19 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 187,253 PSMs, 26,410 peptidoforms and 2,277 protein groups, and the repository holds 17,751 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 187253 where the producer reported 187329 (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 187253 where the producer reported 187329 (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
22.29% of protein intensity in the worst file, 9.85% median across 19 files (DEF-QC-9 v3.5)
22.29% of protein intensity in the worst file, 9.85% median across 19 files (DEF-QC-9 v3.5)
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 52401 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1720 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 52401 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1720 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: 453 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: 453 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. PXD017475:Q641Q2;Q9Y4E1 written 2 times; quant_values: 38 identifier(s), 38 row(s) dropped, e.g. PXD017475:20160617LMH_uLC_0413-18r_MLU_3Ctrl1:label_free:protein_group:PXD017475:Q641Q2;Q9Y4E1: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: 2 identifier(s), 2 row(s) dropped, e.g. PXD017475:Q641Q2;Q9Y4E1 written 2 times; quant_values: 38 identifier(s), 38 row(s) dropped, e.g. PXD017475:20160617LMH_uLC_0413-18r_MLU_3Ctrl1:label_free:protein_group:PXD017475:Q641Q2;Q9Y4E1:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
50 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
50 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 | 187,253 |
| Peptidoforms at 1% FDR | 26,410 |
| Protein groups at 1% FDR | 2,277 |
| PTM sites | 17,751 |
| Quantitative values | 203,728 |
| PSMs, all (including decoys and sub-threshold) | 373,453 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 29.8% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 11.6% |
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
- not recorded
- Runs / samples
- 19 / 19
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 2eb9a52d7f0c
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 4,708 |
| Deamidation on Q | UNIMOD:7 | 1,743 |
| Deamidation on N | UNIMOD:7 | 1,488 |
| Oxidation on M | UNIMOD:35 | 1,483 |
| Carbamyl on K | UNIMOD:5 | 1,001 |
| Carbamyl on X | UNIMOD:5 | 736 |
| Dimethylation on K | UNIMOD:36 | 500 |
| Hydroxylation on P | UNIMOD:35 | 464 |
| Dimethylation on R | UNIMOD:36 | 449 |
| Citrullination on R | UNIMOD:7 | 326 |
| Ammonia loss on N | UNIMOD:385 | 244 |
| Ammonia loss on C | UNIMOD:385 | 222 |
| Carbamyl on M | UNIMOD:5 | 220 |
| Acetylation on K | UNIMOD:1 | 148 |
| Methylation on K | UNIMOD:34 | 134 |
| Trimethylation on K | UNIMOD:37 | 115 |
| N-acetylalanine on A | UNIMOD:1 | 113 |
| Hydroxylation on N | UNIMOD:35 | 112 |
| 4-hydroxyproline on P | UNIMOD:35 | 106 |
| Phosphoserine on S | UNIMOD:21 | 103 |
| Carboxylation on K | UNIMOD:299 | 90 |
| Methylation on R | UNIMOD:34 | 90 |
| Hydroxylation on K | UNIMOD:35 | 89 |
| Phosphorylation on S | UNIMOD:21 | 79 |
| Malonylation on K | UNIMOD:747 | 73 |
| Carboxylation on D | UNIMOD:299 | 67 |
| Carboxylation on E | UNIMOD:299 | 64 |
| N-acetylserine on S | UNIMOD:1 | 57 |
| Carbamyl on R | UNIMOD:5 | 54 |
| N6-acetyllysine on K | UNIMOD:1 | 51 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 48 |
| Phosphorylation on T | UNIMOD:21 | 46 |
| Cu[I] on E | UNIMOD:531 | 43 |
| Carbamyl on C | UNIMOD:5 | 42 |
| Glutarylation on K | UNIMOD:1848 | 42 |
| Water Loss on E | UNIMOD:27 | 41 |
| Cu[I] on D | UNIMOD:531 | 39 |
| Succinylation on K | UNIMOD:64 | 38 |
| Formylation on K | UNIMOD:122 | 34 |
| Zinc on D | UNIMOD:954 | 32 |
| N-acetylmethionine on M | UNIMOD:1 | 31 |
| Sodium on D | UNIMOD:30 | 26 |
| Sulfonation on Y | UNIMOD:40 | 26 |
| Magnesium on D | UNIMOD:956 | 25 |
| Nitrosylation on Y | UNIMOD:354 | 22 |
| Zinc on E | UNIMOD:954 | 20 |
| HexNAc on T | UNIMOD:43 | 18 |
| Acetylation on X | UNIMOD:1 | 17 |
| Deamidated asparagine on N | UNIMOD:7 | 17 |
| Butyrylation on K | UNIMOD:1289 | 16 |
| Hydroxybutyrylation on K | — | 16 |
| Phosphothreonine on T | UNIMOD:21 | 16 |
| Magnesium on E | UNIMOD:956 | 15 |
| N-acetylthreonine on T | UNIMOD:1 | 14 |
| N6-methyllysine on K | UNIMOD:34 | 14 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 13 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 13 |
| Nitrosylation on C | UNIMOD:275 | 13 |
| Phosphorylation on Y | UNIMOD:21 | 13 |
| Sodium on E | UNIMOD:30 | 12 |
| Fe[II] on D | UNIMOD:952 | 11 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 11 |
| HexNAc on S | UNIMOD:43 | 9 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 9 |
| Calcium on D | UNIMOD:951 | 8 |
| Fe[II] on E | UNIMOD:952 | 8 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 8 |
| Omega-N-methylarginine on R | UNIMOD:34 | 8 |
| 5-hydroxylysine on K | UNIMOD:35 | 6 |
| Calcium on E | UNIMOD:951 | 6 |
| N6-crotonyllysine on K | — | 6 |
| N6-succinyllysine on K | — | 6 |
| Potassium on D | UNIMOD:530 | 6 |
| Fe[III] on E | UNIMOD:1870 | 5 |
| Phosphotyrosine on Y | UNIMOD:21 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Fe[III] on D | UNIMOD:1870 | 4 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| Crotonylation on K | UNIMOD:1363 | 3 |
| N6-methacryllysine on K | — | 3 |
| Potassium on E | UNIMOD:530 | 3 |
| Tele-methylhistidine on H | UNIMOD:34 | 3 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| Pyridoxal phosphate on K | UNIMOD:46 | 2 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-malonyllysine 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
65cf99f613971fa0, written 2026-10-29T09:15:00+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