Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics

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Title:	Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics
Authors:	張彙音;Choong, Wai-Kok;Chang, Hui-Yin;Chen, Ching-Tai;Tsai, Chia-Feng;Hsu, Wen-Lian;Chen, Yu-Ju;Sung, Ting-Yi
Contributors:	生醫理工學院生醫科學與工程學系
Keywords:	Amino Acid Sequence;Annexins - chemistry;Annexins - genetics;antibodies;Computational Biology - methods;Computer Simulation;Databases, Protein;G-protein coupled receptors;Genetic Variation;Humans;Hydrophobic and Hydrophilic Interactions;Mass Spectrometry;Molecular Sequence Annotation;Molecular Sequence Data;olfactory receptors;Peptide Fragments - chemistry;Peptide Fragments - genetics;Peptide Fragments - isolation & purification;peptides;Proteolysis;proteome;Proteome - chemistry;Proteome - genetics;Proteome - isolation & purification;proteomics;Proteomics - methods;Proteomics - statistics & numerical data;Receptors, Odorant - chemistry;Receptors, Odorant - genetics;Receptors, Odorant - isolation & purification
Date:	2015-12-04
Issue Date:	2026-04-23 11:16:28 (UTC+8)
Publisher:	American Chemical Society;United States: American Chemical Society
Abstract:	摘要： Protein experiment evidence at protein level from mass spectrometry and antibody experiments are essential to characterize the human proteome. neXtProt (2014-09 release) reported 20 055 human proteins, including 16 491 proteins identified at protein level and 3564 proteins unidentified. Excluding 616 proteins at uncertain level, 2948 proteins were regarded as missing proteins. Missing proteins were unidentified partially due to MS limitations and intrinsic properties of proteins, for example, only appearing in specific diseases or tissues. Despite such reasons, it is desirable to explore issues affecting validation of missing proteins from an “ideal” shotgun analysis of human proteome. We thus performed in silico digestions on the human proteins to generate all in silico fully digested peptides. With these presumed peptides, we investigated the identification of proteins without any unique peptide, the effect of sequence variants on protein identification, difficulties in identifying olfactory receptors, and highly similar proteins. Among all proteins with evidence at transcript level, G protein-coupled receptors and olfactory receptors, based on InterPro classification, were the largest families of proteins and exhibited more frequent variants. To identify missing proteins, the above analyses suggested including sequence variants in protein FASTA for database searching. Furthermore, evidence of unique peptides identified from MS experiments would be crucial for experimentally validating missing proteins. 其他題名： J. Proteome Res 出版者： United States: American Chemical Society 出版日期： 2015-12-04 出處： Journal of proteome research, 2015-12, Vol.14 (12), p.5396-5407 資源來源： ACS 版權： Copyright © 2015 American Chemical Society 識別號： ISSN: 1535-3893 識別號： ISSN: 1535-3907 識別號： EISSN: 1535-3907 識別號： DOI: 10.1021/acs.jproteome.5b00482 識別號： PMID: 26549055
Appears in Collections:	[Department of Biomedical Sciences and Engineering ] journal & Dissertation

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