Dataset Information

Human bladder,colon,kidney,liver cancer LC MS/MS

ABSTRACT: We propose that enrichment of low-abundance proteins benefits MPs finding. ProteoMinerTM is an equalizing technique by reducing high-abundance proteins and enriching low-abundance proteins in biological liquids. With triton X-100/TBS buffer extraction, ProteoMinerTM enrichment and peptide fractionation, 25 MPs with 73 unique peptides were identified from four human tissues, including 10 membrane proteins and 6 nucleus proteins. Then 18 MPs were confirmed with at least 2 unique peptide identification and 6 MPs were confirmed with 1 unique peptide identification by PRM assay. Hence these results demonstrated ProteoMinerTM as a powerful means in discovery of MPs.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Siqi Liu

PROVIDER: MSV000081649 | MassIVE | Wed Oct 25 16:51:00 BST 2017

SECONDARY ACCESSION(S): PXD006833

REPOSITORIES: MassIVE

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Publications

Digging More Missing Proteins Using an Enrichment Approach with ProteoMiner.

Li Siqi S He Yanbin Y Lin Zhilong Z Xu Shaohang S Zhou Ruo R Liang Feng F Wang Jian J Yang Huanming H Liu Siqi S Ren Yan Y

Journal of proteome research 20171026 12

Human Proteome Project (HPP) aims at mapping entire human proteins with a systematic effort upon all the emerging techniques, which would enhance understanding of human biology and lay a foundation for development of medical applications. Until now, 2563 missing proteins (MPs, PE2-4) are still undetected even using the most sensitive approach of protein detection. Herein, we propose that enrichment of low-abundance proteins benefits MPs finding. ProteoMiner is an equalizing technique by reducing ...[more]

PMID: 28960076

Similar Datasets

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.