Generated summary
PXD020462 is a DDA label-free dataset (Homo sapiens) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 4,035 PSMs, 457 peptidoforms and 46 protein groups, and the repository holds 448 PTM sites for it. 7 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, 7 warnings and 1 for information
calibration_failed warning
GPTMD/search ran on uncalibrated spectra (S7)
GPTMD/search ran on uncalibrated spectra (S7)
cysteine_poor warning
3.71% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
3.71% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
high_contamination warning
5.94% of protein intensity in the worst file, 0.02% median across 15 files (DEF-QC-9 v3.5)
5.94% of protein intensity in the worst file, 0.02% median across 15 files (DEF-QC-9 v3.5)
low_core_use warning
14.52 avg cores of 32 allowed (S5)
14.52 avg cores of 32 allowed (S5)
low_id_rate warning
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 4035/325092 = 1.24% of MS2 identified (S3)
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 4035/325092 = 1.24% of MS2 identified (S3)
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.
peptide_rows_localization_ambiguous warning
54 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 129 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `EGPVGLPGIDGR[Common Biological:Dimethylation on R]PGPIGPAGARGE[Metal:Magnesium on E]PGNIGFPGPK|EGPVGLPGID[Metal:Magnesium on D]GR[Common Biological:Dimethylation on R]PGPIGPAGARGEPGNIGFPGPK`, `EGPVGLP[Common Biological:Hydroxylation on P]GIDGRPGP[Common Biological:Hydroxylation on P]IGPAGAR|EGPVGLP[Common Biological:Hydroxylation on P]GIDGRP[Common Biological:Hydroxylation on P]GPIGPAGAR`, `GADGSPGKDGVRGLTGPIGPPGPAGAPGDK[Common Biological:Acetylation on K]GE[Metal:Potassium on E]SGPSGPAGPTGAR|GADGSPGKDGVRGLTGPIGPPGPAGAPGD[Metal:Potassium on D]K[Common Biological:Acetylation on K]GESGPSGPAGPTGAR`.
54 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 129 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `EGPVGLPGIDGR[Common Biological:Dimethylation on R]PGPIGPAGARGE[Metal:Magnesium on E]PGNIGFPGPK|EGPVGLPGID[Metal:Magnesium on D]GR[Common Biological:Dimethylation on R]PGPIGPAGARGEPGNIGFPGPK`, `EGPVGLP[Common Biological:Hydroxylation on P]GIDGRPGP[Common Biological:Hydroxylation on P]IGPAGAR|EGPVGLP[Common Biological:Hydroxylation on P]GIDGRP[Common Biological:Hydroxylation on P]GPIGPAGAR`, `GADGSPGKDGVRGLTGPIGPPGPAGAPGDK[Common Biological:Acetylation on K]GE[Metal:Potassium on E]SGPSGPAGPTGAR|GADGSPGKDGVRGLTGPIGPPGPAGAPGD[Metal:Potassium on D]K[Common Biological:Acetylation on K]GESGPSGPAGPTGAR`.
occupancy_decoy_groups info
2 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
2 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 | 4,035 |
| Peptidoforms at 1% FDR | 457 |
| Protein groups at 1% FDR | 46 |
| PTM sites | 448 |
| Quantitative values | 2,397 |
| PSMs, all (including decoys and sub-threshold) | 295,851 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 1.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.4% |
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
- 15 / 15
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.13
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v6.xml
- Pipeline commit
- 314f6ae55a6e
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Hydroxylation on P | UNIMOD:35 | 101 |
| 4-hydroxyproline on P | UNIMOD:35 | 72 |
| Deamidation on N | UNIMOD:7 | 33 |
| Oxidation on M | UNIMOD:35 | 31 |
| Deamidation on Q | UNIMOD:7 | 30 |
| Citrullination on R | UNIMOD:7 | 16 |
| Phosphorylation on S | UNIMOD:21 | 16 |
| Sodium on E | UNIMOD:30 | 14 |
| Carbamidomethyl on C | UNIMOD:4 | 13 |
| Magnesium on E | UNIMOD:956 | 11 |
| Methylation on R | UNIMOD:34 | 8 |
| Acetylation on K | UNIMOD:1 | 7 |
| Dimethylation on R | UNIMOD:36 | 7 |
| Hydroxylation on K | UNIMOD:35 | 7 |
| Methylation on K | UNIMOD:34 | 7 |
| Magnesium on D | UNIMOD:956 | 5 |
| Phosphorylation on T | UNIMOD:21 | 5 |
| Sodium on D | UNIMOD:30 | 5 |
| 5-hydroxylysine on K | UNIMOD:35 | 4 |
| Potassium on E | UNIMOD:530 | 4 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| Calcium on E | UNIMOD:951 | 3 |
| Dimethylation on K | UNIMOD:36 | 3 |
| Malonylation on K | UNIMOD:747 | 3 |
| Phosphoserine on S | UNIMOD:21 | 3 |
| Succinylation on K | UNIMOD:64 | 3 |
| Allysine on K | UNIMOD:352 | 2 |
| Ammonia loss on N | UNIMOD:385 | 2 |
| Calcium on D | UNIMOD:951 | 2 |
| Hydroxylation on N | UNIMOD:35 | 2 |
| Potassium on D | UNIMOD:530 | 2 |
| 4-carboxyglutamate on E | UNIMOD:299 | 1 |
| Carboxylation on D | UNIMOD:299 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Fe[II] on E | UNIMOD:952 | 1 |
| Hydroxybutyrylation on K | — | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| N-acetylalanine on A | UNIMOD:1 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| Trimethylation on K | UNIMOD:37 | 1 |
| Water Loss on E | UNIMOD:27 | 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
9f9ab4831550cd4d, written 2026-10-31T19:00:09+00:00 by ingester 1.4.0- Reconciliation
- every check agreed with the producer's own counts
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group