Generated summary
PXD022180 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 118,902 PSMs, 18,717 peptidoforms and 1,853 protein groups, and the repository holds 9,342 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
calibration_failed warning
GPTMD/search ran on uncalibrated spectra (S7)
GPTMD/search ran on uncalibrated spectra (S7)
count_mismatch warning
The bundle holds 118902 where the producer reported 118996 (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 118902 where the producer reported 118996 (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
31.87% of protein intensity in the worst file, 11.15% median across 18 files (DEF-QC-9 v3.5)
31.87% of protein intensity in the worst file, 11.15% median across 18 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 18899 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2809 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 18899 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2809 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: 475 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: 475 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: 1 identifier(s), 1 row(s) dropped, e.g. PXD022180:M0QZD8;Q6ZTK2 written 2 times; quant_values: 19 identifier(s), 19 row(s) dropped, e.g. PXD022180:2020-09-03_GDT_PG_Mytho_IP_HeLa_Bas_1:label_free:protein_group:PXD022180:M0QZD8;Q6ZTK2: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: 1 identifier(s), 1 row(s) dropped, e.g. PXD022180:M0QZD8;Q6ZTK2 written 2 times; quant_values: 19 identifier(s), 19 row(s) dropped, e.g. PXD022180:2020-09-03_GDT_PG_Mytho_IP_HeLa_Bas_1:label_free:protein_group:PXD022180:M0QZD8;Q6ZTK2:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
8 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
8 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 | 118,902 |
| Peptidoforms at 1% FDR | 18,717 |
| Protein groups at 1% FDR | 1,853 |
| PTM sites | 9,342 |
| Quantitative values | 144,906 |
| PSMs, all (including decoys and sub-threshold) | 233,518 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 22.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 6.4% |
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
- immunoprecipitation
- 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-v3.xml
- Pipeline commit
- fbfc3c110165
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 2,799 |
| Oxidation on M | UNIMOD:35 | 1,454 |
| Deamidation on N | UNIMOD:7 | 767 |
| Deamidation on Q | UNIMOD:7 | 570 |
| Fe[III] on E | UNIMOD:1870 | 224 |
| Hydroxylation on P | UNIMOD:35 | 210 |
| N-acetylalanine on A | UNIMOD:1 | 197 |
| Fe[III] on D | UNIMOD:1870 | 189 |
| Fe[II] on E | UNIMOD:952 | 168 |
| Citrullination on R | UNIMOD:7 | 156 |
| Fe[II] on D | UNIMOD:952 | 134 |
| Hydroxylation on N | UNIMOD:35 | 121 |
| Ammonia loss on N | UNIMOD:385 | 104 |
| Hydroxylation on K | UNIMOD:35 | 92 |
| Ammonia loss on C | UNIMOD:385 | 85 |
| N-acetylmethionine on M | UNIMOD:1 | 65 |
| N-acetylserine on S | UNIMOD:1 | 63 |
| Methylation on K | UNIMOD:34 | 57 |
| Sodium on E | UNIMOD:30 | 53 |
| Sodium on D | UNIMOD:30 | 52 |
| Carbamyl on X | UNIMOD:5 | 48 |
| Magnesium on D | UNIMOD:956 | 48 |
| Magnesium on E | UNIMOD:956 | 39 |
| Calcium on D | UNIMOD:951 | 35 |
| Water Loss on E | UNIMOD:27 | 34 |
| Methylation on R | UNIMOD:34 | 29 |
| Dimethylation on K | UNIMOD:36 | 28 |
| N6-acetyllysine on K | UNIMOD:1 | 27 |
| Phosphoserine on S | UNIMOD:21 | 23 |
| Dimethylation on R | UNIMOD:36 | 21 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 19 |
| Carbamyl on K | UNIMOD:5 | 19 |
| Acetylation on X | UNIMOD:1 | 18 |
| Calcium on E | UNIMOD:951 | 18 |
| Acetylation on K | UNIMOD:1 | 17 |
| Formylation on K | UNIMOD:122 | 16 |
| Phosphorylation on S | UNIMOD:21 | 16 |
| N6-methyllysine on K | UNIMOD:34 | 14 |
| N-acetylthreonine on T | UNIMOD:1 | 13 |
| Phosphorylation on T | UNIMOD:21 | 13 |
| Deamidated asparagine on N | UNIMOD:7 | 12 |
| 4-hydroxyproline on P | UNIMOD:35 | 11 |
| Carbamyl on M | UNIMOD:5 | 11 |
| Omega-N-methylarginine on R | UNIMOD:34 | 11 |
| Potassium on D | UNIMOD:530 | 11 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 10 |
| Phosphothreonine on T | UNIMOD:21 | 10 |
| Carboxylation on D | UNIMOD:299 | 8 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 8 |
| Carboxylation on E | UNIMOD:299 | 7 |
| Carboxylation on K | UNIMOD:299 | 7 |
| Hydroxybutyrylation on K | — | 7 |
| N-acetylvaline on V | UNIMOD:1 | 7 |
| N6-succinyllysine on K | — | 7 |
| Nitrosylation on Y | UNIMOD:354 | 7 |
| Crotonylation on K | UNIMOD:1363 | 6 |
| HexNAc on T | UNIMOD:43 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 5 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 5 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Carbamyl on C | UNIMOD:5 | 4 |
| Carbamyl on R | UNIMOD:5 | 4 |
| Malonylation on K | UNIMOD:747 | 4 |
| Nitrosylation on C | UNIMOD:275 | 4 |
| Potassium on E | UNIMOD:530 | 4 |
| Trimethylation on K | UNIMOD:37 | 4 |
| Glutarylation on K | UNIMOD:1848 | 3 |
| HexNAc on S | UNIMOD:43 | 3 |
| N-acetylproline on P | UNIMOD:1 | 3 |
| Phosphorylation on Y | UNIMOD:21 | 3 |
| Phosphotyrosine on Y | UNIMOD:21 | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| Succinylation on K | UNIMOD:64 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-glutaryllysine 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
af56ee3d57d4ccb5, written 2026-10-29T09:34:58+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