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PXD008782

PXD008782 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOpen-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics, part 1
DescriptionShotgun 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.
HostingRepositoryPRIDE
AnnounceDate2018-07-11
AnnouncementXMLSubmission_2018-07-11_08:07:34.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterHao Chi
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-01-29 01:38:51ID requested
12018-07-11 08:07:35announced
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 affiliationInstitute of Computing Technology
contact emailsmhe@ict.ac.cn
lab head
Hao Chi
contact affiliationInstitute of Computing Technology, CAS
contact emailchihao@ict.ac.cn
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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