ACS Publications. Most Trusted. Most Cited. Most Read
Optimization of Microflow LC Coupled with Scanning SWATH and Its Application in Hepatocellular Carcinoma Tissues

OR SEARCH CITATIONS

My Activity
Publications

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Proteome Res. 2022, 21, 7, 1686-1693
    Article

    Optimization of Microflow LC Coupled with Scanning SWATH and Its Application in Hepatocellular Carcinoma Tissues
    Click to copy article linkArticle link copied!

    • Huanhuan Gao
      Huanhuan Gao
      Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China
      Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
      More by Huanhuan Gao
    • Youqi Liu
      Youqi Liu
      Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No. 1 Yunmeng Road, Cloud Town, Xihu District, Hangzhou 310024, Zhejiang Province, China
      More by Youqi Liu
    • Vadim Demichev
      Vadim Demichev
      Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London WC2N 5DU, U.K.
      Department of Biochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin 10115, Germany
      More by Vadim Demichev
    • Stephen Tate
      Stephen Tate
      SCIEX, Concord, Ontario L4K 4V8, Canada
      More by Stephen Tate
      Orcidhttps://orcid.org/0000-0001-5508-0819
    • Chen Chen
      Chen Chen
      SCIEX, Shanghai 200000, China
      More by Chen Chen
    • Jiang Zhu
      Jiang Zhu
      Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, Hubei, China
      More by Jiang Zhu
    • Cong Lu
      Cong Lu
      Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, Hubei, China
      More by Cong Lu
    • Markus Ralser
      Markus Ralser
      Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London WC2N 5DU, U.K.
      Department of Biochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin 10115, Germany
      More by Markus Ralser
      Orcidhttps://orcid.org/0000-0001-9535-7413
    • Tiannan Guo*
      Tiannan Guo
      Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China
      Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
      *Email: [email protected]
      More by Tiannan Guo
      Orcidhttps://orcid.org/0000-0003-3869-7651
    • Yi Zhu*
      Yi Zhu
      Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China
      Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
      *Email: [email protected]
      More by Yi Zhu
      Orcidhttps://orcid.org/0000-0003-0429-0802
    Other Access OptionsSupporting Information (5)

    Journal of Proteome Research

    Cite this: J. Proteome Res. 2022, 21, 7, 1686–1693
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jproteome.2c00078
    Published June 2, 2022
    Copyright © 2022 American Chemical Society
    Request reuse permissions

    Abstract

    Click to copy section linkSection link copied!
    Abstract Image

    Scanning SWATH coupled with normal-flow LC has been recently introduced for high-content, high-throughput proteomics analysis, which requires a relatively large amount of sample injection. Here we established the microflow LC coupled with Scanning SWATH for samples with relatively small quantities. First, we optimized several key parameters of the LC and MS settings, including C18 particle size for the analytical column, LC gradient and flow rate, as well as effective ion accumulation time and isolation window width for MS acquisition. We then compared the optimized Scanning SWATH method with the conventional variable window SWATH (referred to as SWATH) method. Results showed that the total ion chromatogram signals in Scanning SWATH were 10 times higher than that of SWATH, and Scanning SWATH identified 12.2–22.2% more peptides than SWATH. Finally, we employed 120 min Scanning SWATH to acquire the proteomes of 62 formalin-fixed, paraffin-embedded (FFPE) tissue samples from 31 patients with hepatocellular carcinoma (HCC). Altogether, 92 334 peptides and 8516 proteins were quantified. Besides the reported biomarkers, including ANXA2, MCM7, SUOX, and AKR1B10, we identified new potential HCC biomarkers such as CST5, TP53, CEBPB, and E2F4. Taken together, we present an optimal workflow integrating microflow LC and Scanning SWATH that effectively improves the protein identification and quantitation.

    Copyright © 2022 American Chemical Society

    Subjects

    what are subjects

    Keywords

    what are keywords

    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. Add or change your institution or let them know you’d like them to include access.

    Supporting Information

    Click to copy section linkSection link copied!

    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00078.

    • Table S1: LC-MS parameters of Scanning SWATH and SWATH (XLSX)

    • Table S2: Clinical information and protein matrix of the HCC cohort (XLSX)

    • Table S3: The ratio of the missing values in the quantitative proteome of 31 pairs of HCC samples (XLSX)

    • Table S4: IPA of 1730 dysregulated proteins from the 31 patients with HCC (XLSX)

    • Figure S1: Distribution of identified proteins and relevant abundance as calculated by MS2 intensities from SWATH and Scanning SWATH; Figure S2: The distribution of peptide and protein identifications of the HCC proteomes (PDF)

    Terms & Conditions

    Electronic Supporting Information files are available without a subscription to ACS Web Editions. The American Chemical Society holds a copyright ownership interest in any copyrightable Supporting Information. Files available from the ACS website may be downloaded for personal use only. Users are not otherwise permitted to reproduce, republish, redistribute, or sell any Supporting Information from the ACS website, either in whole or in part, in either machine-readable form or any other form without permission from the American Chemical Society. For permission to reproduce, republish and redistribute this material, requesters must process their own requests via the RightsLink permission system. Information about how to use the RightsLink permission system can be found at http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    Click to copy section linkSection link copied!
    Citation Statements
    Explore this article's citation statements on scite.ai
    powered by  Scite

    This article is cited by 5 publications.

    1. Kongxin Gu, Haruka Kumabe, Takumi Yamamoto, Naoto Tashiro, Takeshi Masuda, Shingo Ito, Sumio Ohtsuki. Improving Proteomic Identification Using Narrow Isolation Windows with Zeno SWATH Data-Independent Acquisition. Journal of Proteome Research 2024, 23 (8) , 3484-3495. https://doi.org/10.1021/acs.jproteome.4c00149
    2. Mukul K. Midha, Charu Kapil, Michal Maes, David H. Baxter, Seamus R. Morrone, Timothy J. Prokop, Robert L. Moritz. Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker timsTOF Mass Spectrometer. Journal of Proteome Research 2023, 22 (7) , 2525-2537. https://doi.org/10.1021/acs.jproteome.3c00305
    3. Kang Liu, Zitong Chen, Lishan Liu, Ting Li, Changying Xing, Feng Han, Huijuan Mao. Causal Effects of Oxidative Stress on Diabetes Mellitus and Microvascular Complications: Insights Integrating Genome-Wide Mendelian Randomization, DNA Methylation, and Proteome. Antioxidants 2024, 13 (8) , 903. https://doi.org/10.3390/antiox13080903
    4. Lisa Schweizer, Tina Schaller, Maximilian Zwiebel, Özge Karayel, Johannes Bruno Müller‐Reif, Wen‐Feng Zeng, Sebastian Dintner, Thierry M Nordmann, Klaus Hirschbühl, Bruno Märkl, Rainer Claus, Matthias Mann. Quantitative multiorgan proteomics of fatal COVID‐19 uncovers tissue‐specific effects beyond inflammation. EMBO Molecular Medicine 2023, 15 (9) https://doi.org/10.15252/emmm.202317459
    5. Mukul K. Midha, Charu Kapil, Michal Maes, David H. Baxter, Seamus R. Morrone, Timothy J. Prokop, Robert L. Moritz. Vacuum Insulated Probe Heated ElectroSpray Ionization source (VIP-HESI) enhances micro flow rate chromatography signals in the Bruker timsTOF mass spectrometer. 2023https://doi.org/10.1101/2023.02.15.528699
    6. Lisa Schweizer, Tina Schaller, Maximilian Zwiebel, Özge Karayel, Johannes B. Müller-Reif, Wen-Feng Zeng, Sebastian Dintner, Klaus Hirschbühl, Bruno Märkl, Rainer Claus, Matthias Mann. Quantitative multi-organ proteomics of fatal COVID-19 uncovers tissue-specific effects beyond inflammation. 2022https://doi.org/10.1101/2022.12.21.22283785
    7. Yangyang Bian, Chunli Gao, Bernhard Kuster. On the potential of micro-flow LC-MS/MS in proteomics. Expert Review of Proteomics 2022, 19 (3) , 153-164. https://doi.org/10.1080/14789450.2022.2134780
    Download PDF
    Go to Journal of Proteome Research
    Get e-Alerts
    Get e-Alerts

    Journal of Proteome Research

    Cite this: J. Proteome Res. 2022, 21, 7, 1686–1693
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jproteome.2c00078
    Published June 2, 2022
    Copyright © 2022 American Chemical Society
    Request reuse permissions

    Article Views

    1199

    Altmetric

    -

    Citations

    5
    Learn about these metrics

    Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

    Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

    The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.