PXD022280 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Spectral prediction features as a solution for the search space size problem in proteogenomics |
Description | Proteogenomics approaches often struggle with the distinction between right and false peptide-to-spectrum matches as the database size enlarges. However, features extracted from tandem mass spectrometry intensity predictors can enhance the peptide identification rate and can provide extra confidence for spectral matching in a proteogenomic context. To that end, features from the spectral intensity pattern predictors MS2PIP and Prosit were combined with the canonical scores from MaxQuant in the Percolator post-processing tool for protein databases constructed from RNA-seq and ribosome profiling analyses. The presented results provide evidence that this approach enhances the peptide identification power in a proteogenomic setting and in the meantime they lead to the validation of new proteoforms with elevated stringency. In this online repository, we submitted the conventional proteomic search results with MaxQuant against the custom nanopore RNA-seq-based search space. All other results can be found in the supplemental materials of the manuscript, in SRA (sequencing data) or under ProteomeXChange Project PXD011353 (as this is original data from a previuos paper). |
HostingRepository | PRIDE |
AnnounceDate | 2023-05-14 |
AnnouncementXML | Submission_2023-05-14_14:15:38.166.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | StevenVerbruggen |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | acetylated residue; monohydroxylated residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-11-02 00:01:47 | ID requested | |
1 | 2021-03-26 05:26:07 | announced | |
2 | 2021-04-07 05:29:20 | announced | 2021-04-07: Updated publication reference for PubMed record(s): 31040227, 33823297. |
3 | 2021-04-07 21:57:13 | announced | 2021-04-08: Updated project metadata. |
4 | 2021-04-07 21:59:38 | announced | 2021-04-08: Updated project metadata. |
⏵ 5 | 2023-05-14 14:15:39 | announced | 2023-05-14: Updated project metadata. |
Publication List
Verbruggen S, Gessulat S, Gabriels R, Matsaroki A, Van de Voorde H, Kuster B, Degroeve S, Martens L, Van Criekinge W, Wilhelm M, Menschaert G, Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics. Mol Cell Proteomics, 20():100076(2021) [pubmed] |
Keyword List
ProteomeXchange project tag: EPIC-XS |
submitter keyword: proteogenomics |
spectrum predictor |
nanopore sequencing |
ribosome profiling |
RNA-seq |
MS2PIP |
Prosit |
intensity features |
machine learning |
HCT116 |
Percolator |
MaxQuant |
Contact List
GerbenMenschaert |
contact affiliation | BioBix, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, Belgium |
contact email | Gerben.Menschaert@UGent.be |
lab head | |
StevenVerbruggen |
contact affiliation | BioBix |
contact email | Steven.Verbruggen@UGent.be |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/03/PXD022280 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD022280
- Label: PRIDE project
- Name: Spectral prediction features as a solution for the search space size problem in proteogenomics