ACS Publications. Most Trusted. Most Cited. Most Read
My Activity
CONTENT TYPES

MS1-Level Proteome Quantification Platform Allowing Maximally Increased Multiplexity for SILAC and In Vitro Chemical Labeling

  • Yeon Choi
    Yeon Choi
    Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
    School of Biological Sciences, Seoul National University, Seoul 08826, Korea
    More by Yeon Choi
  • Kyowon Jeong
    Kyowon Jeong
    Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
    School of Biological Sciences, Seoul National University, Seoul 08826, Korea
    More by Kyowon Jeong
  • Sanghee Shin
    Sanghee Shin
    Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
    School of Biological Sciences, Seoul National University, Seoul 08826, Korea
    More by Sanghee Shin
  • Joon Won Lee
    Joon Won Lee
    Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
    More by Joon Won Lee
  • Young-suk Lee
    Young-suk Lee
    Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
    School of Biological Sciences, Seoul National University, Seoul 08826, Korea
  • Sangtae Kim
    Sangtae Kim
    Illumina, Inc., San Diego, California 92122, United States
    More by Sangtae Kim
  • Sun Ah Kim
    Sun Ah Kim
    Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
    School of Biological Sciences, Seoul National University, Seoul 08826, Korea
    More by Sun Ah Kim
  • Jaehun Jung
    Jaehun Jung
    Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
    More by Jaehun Jung
  • Kwang Pyo Kim
    Kwang Pyo Kim
    Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
  • V. Narry Kim*
    V. Narry Kim
    Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
    School of Biological Sciences, Seoul National University, Seoul 08826, Korea
    *Email: [email protected]
    More by V. Narry Kim
  • , and 
  • Jong-Seo Kim*
    Jong-Seo Kim
    Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
    School of Biological Sciences, Seoul National University, Seoul 08826, Korea
    *Email: [email protected]
    More by Jong-Seo Kim
Cite this: Anal. Chem. 2020, 92, 7, 4980–4989
Publication Date (Web):March 13, 2020
https://doi.org/10.1021/acs.analchem.9b05148
Copyright © 2020 American Chemical Society

    Article Views

    1389

    Altmetric

    -

    Citations

    LEARN ABOUT THESE METRICS
    Other access options
    Supporting Info (8)»

    Abstract

    Abstract Image

    Quantitative proteomic platforms based on precursor intensity in mass spectrometry (MS1-level) uniquely support in vivo metabolic labeling with superior quantification accuracy but suffer from limited multiplexity (≤3-plex) and frequent missing quantities. Here we present a new MS1-level quantification platform that allows maximal multiplexing with high quantification accuracy and precision for the given labeling scheme. The platform currently comprises 6-plex in vivo SILAC or in vitro diethylation labeling with a dedicated algorithm and is also expandable to higher multiplexity (e.g., nine-plex for SILAC). For complex samples with broad dynamic ranges such as total cell lysates, our platform performs highly accurately and free of missing quantities. Furthermore, we successfully applied our method to measure protein synthesis rate under heat shock response in human cells by 6-plex pulsed SILAC experiments, demonstrating the unique biological merits of our in vivo platform to disclose translational regulations for cellular response to stress.

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. You can change your affiliated institution below.

    Supporting Information

    ARTICLE SECTIONS
    Jump To

    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.analchem.9b05148.

    • Supplementary figures, supplementary table list, detailed materials and experimental procedures, and detailed description on bioinformatic algorithms used in this paper (supplementary algorithm notes) (PDF)

    • Table S1. SILAC-6plex 5:2:10:1:10:20 proteins (related to Figure 3A,C) (XLSX)

    • Table S2. DE-6plex 20:10:1:10:2:5 proteins (related to Figure 3B,D) (XLSX)

    • Table S3. Medians and standard deviations of protein-level fold changes (related to Figure 3C,D) (XLSX)

    • Table S4. SILAC-6plex 20:10:1:10:2:5 PSMs, by EPIQ (related to Figure S8A) (XLSX)

    • Table S5. DE-6plex 20:10:1:10:2:5 PSMs, by EPIQ (related to Figure S8B) (XLSX)

    • Table S6. DEP analysis on protein groups, by EPIQ (related to Figures 3E,F and S9) (XLSX)

    • Table S7. Analysis on protein dynamics of HeLa cells under HSR (related to Figure 4) (XLSX)

    Accession Codes

    The source codes of EPIQ and its usage guide are freely accessible though GitHub (https://github.com/YeonChoi/EPIQ). All of the original LC-MS/MS data sets and related identification files used to support this paper have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (38) with the data set identifier <PXD009952>.

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    This article is cited by 1 publications.

    1. Xiaobo Tian, Hjalmar P. Permentier, Rainer Bischoff. Chemical isotope labeling for quantitative proteomics. Mass Spectrometry Reviews 2023, 42 (2) , 546-576. https://doi.org/10.1002/mas.21709

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    MENDELEY PAIRING EXPIRED
    Your Mendeley pairing has expired. Please reconnect