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        Proteoform 분석을 위한 탑다운 단백체학 기술 개발 연구동향

        유지원,김민주,박해민 한국생물공학회 2023 KSBB Journal Vol.38 No.1

        Over the past decade, mass spectrometry-based bottom-up proteomics (BUP) has been widely used to identify and to quantify complete proteomes from a biological system such as a cell, tissue, or organism. However, due to the protein inference problem, BUP approaches have intrinsic limitations for identifying and characterizing intact proteins that underlie complex traits and molecular mechanisms in biology. In contrast to BUP, which measures peptides produced from proteins by proteolytic digestion, top-down proteomics (TDP) is a powerful technology that allows for measuring intact proteins without proteolysis, thus identifying and quantifying proteoforms which provide new insights into molecular mechanisms. A proteoform is a defined form of a protein product from a single gene, including combinatorial coding polymorphisms, alternative RNA splicing events, and post-translational modifications (PTMs) on the same molecule. In this review, we outline some advances in separation, ionization, and fragmentation of intact proteins and data processing for TDP along with the growing power of proteoform- resolved measurements in clinical and translational research and biotechnology.

      • Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function

        Paik, Young-Ki,Lane, Lydie,Kawamura, Takeshi,Chen, Yu-Ju,Cho, Je-Yoel,LaBaer, Joshua,Yoo, Jong Shin,Domont, Gilberto,Corrales, Fernando,Omenn, Gilbert S.,Archakov, Alexander,Encarnació,n-Guevara American Chemical Society 2018 JOURNAL OF PROTEOME RESEARCH Vol.17 No.12

        <P>An important goal of the Human Proteome Organization (HUPO) Chromosome-centric Human Proteome Project (C-HPP) is to correctly define the number of canonical proteins encoded by their cognate open reading frames on each chromosome in the human genome. When identified with high confidence of protein evidence (PE), such proteins are termed PE1 proteins in the online database resource, neXtProt. However, proteins that have not been identified unequivocally at the protein level but that have other evidence suggestive of their existence (PE2-4) are termed missing proteins (MPs). The number of MPs has been reduced from 5511 in 2012 to 2186 in 2018 (neXtProt 2018-01-17 release). Although the annotation of the human proteome has made significant progress, the “parts list” alone does not inform function. Indeed, 1937 proteins representing ∼10% of the human proteome have no function either annotated from experimental characterization or predicted by homology to other proteins. Specifically, these 1937 “dark proteins” of the so-called dark proteome are composed of 1260 functionally uncharacterized but identified PE1 proteins, designated as uPE1, plus 677 MPs from categories PE2-PE4, which also have no known or predicted function and are termed uMPs. At the HUPO-2017 Annual Meeting, the C-HPP officially adopted the uPE1 pilot initiative, with 14 participating international teams later committing to demonstrate the feasibility of the functional <U>c</U>haracterization of large numbers of dark <U>p</U>roteins (CP), starting first with 50 uPE1 proteins, in a stepwise chromosome-centric organizational manner. The second aim of the feasibility phase to <U>c</U>haracterize protein (CP) functions of 50 uPE1 proteins, termed the neXt-CP50 initiative, is to utilize a variety of approaches and workflows according to individual team expertise, interest, and resources so as to enable the C-HPP to recommend experimentally proven workflows to the proteome community within 3 years. The results from this pilot will not only be the cornerstone of a larger characterization initiative but also enhance understanding of the human proteome and integrated cellular networks for the discovery of new mechanisms of pathology, mechanistically informative biomarkers, and rational drug targets.</P> [FIG OMISSION]</BR>

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