PXD015759

PXD015759 is an original dataset announced via ProteomeXchange.

Title	Open-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue
Description	In recent years, high-throughput technologies have contributed to development a more precise picture of the human proteome. However, 2,129 proteins remain listed as missing proteins (MPs) in the newest neXtProt release (2019-02). The main reasons for MPs are a low abundance, low-molecular-weight (LMW), unexpected modifications, membrane characteristics, etc. Moreover, more than 50% of the MS/MS data have not been successfully identified in shotgun proteomics. Open-pFind, an efficient open search engine, recently released by the pFind group in China, presents an opportunity to identify these buried MPs in complex samples. Proteins and potential MPs were identified using Open-pFind and three other search engines to compare their performance and efficiency with three large-scale datasets digested by different enzymes. Our results demonstrated that Open-pFind identified 29.9-47.5% more peptide-spectrum matches (PSMs), 48.0-63.9% more peptides sequences (with modifications) and 22.7-38.1% more peptide sequences (regardless of modifications) than those identified by the second-best search engine. As a result, Open-pFind detected 7.5-19.3% more candidate MPs than those by the second-best search engine. In total, 5 (PE2) of the 150 candidate MPs identified by Open-pFind were verified from two unique peptides containing more than 9 amino acids (AA) by using spectrum theoretical prediction with pDeep, and synthesized peptide matching with pBuild, after spectrum quality analysis, isobaric post-translational modification, and single amino acid variant (SAAV) filtering. These five verified MPs can be ranked in the PE1 level. In addition, three other candidate MPs were verified with two unique peptides (one peptide containing more than 9 AA) and the other containing only 8 AA), which were slightly lower than the criteria listed by C-HPP, and required additional verification information. More importantly, unexpected modifications were detected in these MPs. Another 141 MPs were listed as candidates, but required additional verification information.
HostingRepository	PRIDE
AnnounceDate	2019-11-04
AnnouncementXML	Submission_2019-11-04_06:29:49.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sun jinshuai
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-09 07:59:23	ID requested
⏵ 1	2019-11-04 06:29:50	announced

Sun J, Shi J, Wang Y, Wu S, Zhao L, Li Y, Wang H, Chang L, Lyu Z, Wu J, Liu F, Li W, He F, Zhang Y, Xu P, Open-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue. J Proteome Res, 18(12):4189-4196(2019) [pubmed]

ProteomeXchange project tag: Chromosome-centric Human Proteome Project (C-HPP), China Human Proteome Project (CNHPP), Human Proteome Project

submitter keyword: Chromosome-Centric Human Proteome Project, missing proteins, testis, Open-pFind，efficiency

Ping Xu
contact affiliation	Ping Xu, Ph.D. Secretary General of CNHUPO Professor, Director Department of Genomics and Proteomics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics， 38 Life Science Park Road, Beijing 102206, P.R. China. Tel: 0086-10-61777113, Fax: 0086-10-61777060
contact email	xuping_bprc@126.com
lab head
Sun jinshuai
contact affiliation	Student
contact email	sjsshuai@126.com
dataset submitter

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/2019/11/PXD015759

PRIDE project URI

• PRIDE
  1. PXD015759
     1. Label: PRIDE project
     2. Name: Open-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue