PXD008782 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Open-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics, part 1 |
Description | Shotgun proteomics has grown rapidly in recent decades, but a large fraction of tandem mass spectrometry (MS/MS) data in shotgun proteomics are not successfully identified. We have developed a novel database search algorithm, Open-pFind, to efficiently identify peptides even in an ultra-large search space which takes into account unexpected modifications, amino acid mutations, semi- or non-specific digestion and co-eluting peptides. Tested on two metabolically labeled MS/MS datasets, Open-pFind reported 50.5‒117.0% more peptide-spectrum matches (PSMs) than the seven other advanced algorithms. More importantly, the Open-pFind results were more credible judged by the verification experiments using stable isotopic labeling. Tested on four additional large-scale datasets, 70‒85% of the spectra were confidently identified, and high-quality spectra were nearly completely interpreted by Open-pFind. Further, Open-pFind was over 40 times faster than the other three open search algorithms and 2‒3 times faster than three restricted search algorithms. Re-analysis of an entire human proteome dataset consisting of ~25 million spectra using Open-pFind identified a total of 14,064 proteins encoded by 12,723 genes by requiring at least two uniquely identified peptides. In this search results, Open-pFind also excelled in an independent test for false positives based on the presence or absence of olfactory receptors. Thus, a practical use of the open search strategy has been realized by Open-pFind for the truly global-scale proteomics experiments of today and in the future. |
HostingRepository | PRIDE |
AnnounceDate | 2018-07-11 |
AnnouncementXML | Submission_2018-07-11_08:07:34.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Hao Chi |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-01-29 01:38:51 | ID requested | |
⏵ 1 | 2018-07-11 08:07:35 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
curator keyword: Technical |
submitter keyword: Open-pFind, E. coli, Yeast, Metabolically label |
Contact List
Si-Min He |
contact affiliation | Institute of Computing Technology |
contact email | smhe@ict.ac.cn |
lab head | |
Hao Chi |
contact affiliation | Institute of Computing Technology, CAS |
contact email | chihao@ict.ac.cn |
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/2018/07/PXD008782 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD008782
- Label: PRIDE project
- Name: Open-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics, part 1