title: Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics.
abstract: 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.
authors.affiliation: Institute of Information Science, Academia Sinica , Taipei 11529, Taiwan.
authors.forename: Wai-Kok
authors.initials: WK
authors.lastname: Choong
authors.affiliation: Institute of Information Science, Academia Sinica , Taipei 11529, Taiwan.|Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica , Taipei 11529, Taiwan.|Institute of Biomedical Informatics, National Yang-Ming University , Taipei 11221, Taiwan.
authors.forename: Hui-Yin
authors.initials: HY
authors.lastname: Chang
authors.affiliation: Institute of Information Science, Academia Sinica , Taipei 11529, Taiwan.
authors.forename: Ching-Tai
authors.initials: CT
authors.lastname: Chen
authors.affiliation: Institute of Chemistry, Academia Sinica , Taipei 11529, Taiwan.
authors.forename: Chia-Feng
authors.initials: CF
authors.lastname: Tsai
authors.affiliation: Institute of Information Science, Academia Sinica , Taipei 11529, Taiwan.
authors.forename: Wen-Lian
authors.initials: WL
authors.lastname: Hsu
authors.affiliation: Institute of Chemistry, Academia Sinica , Taipei 11529, Taiwan.
authors.forename: Yu-Ju
authors.initials: YJ
authors.lastname: Chen
authors.affiliation: Institute of Information Science, Academia Sinica , Taipei 11529, Taiwan.
authors.forename: Ting-Yi
authors.initials: TY
authors.lastname: Sung
mesh_terms: D000595:Amino Acid Sequence; D017302:Annexins / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D030562:Databases, Protein; D014644:Genetic Variation; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D013058:Mass Spectrometry; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D059748:Proteolysis; D020543:Proteome / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data; D018035:Receptors, Odorant / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification
chemical_list: D017302:Annexins; D010446:Peptide Fragments; D020543:Proteome; D018035:Receptors, Odorant
keywords: in silico digestion; missing proteins; olfactory receptors; sequence variation; unique peptide