Dataset Information

Human Testis LC-MS/MS - Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue

ABSTRACT: Missing proteins(MPs) investigation is one of the critical missions of Chromosome-based Human Proteome Project(C-HPP). Through analyzing sequence of MPs from neXtProt database, we found that there are no detectable tryptic peptides for some MPs. Here, we attmept a multi-enzymes strategy to cover this problem. Lys-C, Glu-C and LysargiNase are used to produce more unique and detectable peptides of MPs.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Testis

SUBMITTER: Yihao Wang

LAB HEAD: Ping Xu

PROVIDER: PXD006465 | Pride | 2017-10-09

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	170325_HF02_XuPing_CNHPP_A_GluC_1_F1_R1.raw	Raw
	170325_HF02_XuPing_CNHPP_A_GluC_2_F1_R1.raw	Raw
	170325_HF02_XuPing_CNHPP_A_GluC_3_F1_R1.raw	Raw
	170325_HF02_XuPing_CNHPP_A_GluC_4_F1_R1.raw	Raw
	170325_HF02_XuPing_CNHPP_A_GluC_5_F1_R1.raw	Raw

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Publications

Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue.

Wang Yihao Y Chen Yang Y Zhang Yao Y Wei Wei W Li Yanchang Y Zhang Tao T He Fuchu F Gao Yue Y Xu Ping P

Journal of proteome research 20171013 12

Although 5 years of the missing proteins (MPs) study have been completed, searching for MPs remains one of the core missions of the Chromosome-Centric Human Proteome Project (C-HPP). Following the next-50-MPs challenge of the C-HPP, we have focused on the testis-enriched MPs by various strategies since 2015. On the basis of the theoretical analysis of MPs (2017-01, neXtProt) using multiprotease digestion, we found that nonconventional proteases (e.g. LysargiNase, GluC) could improve the peptide ...[more]

PMID: 28959888

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Project 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.

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