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Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Proteome Res. 2019, 18, 10, 3800-3806
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    Common Repository of FBS Proteins (cRFP) To Be Added to a Search Database for Mass Spectrometric Analysis of Cell Secretome
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    • Jihye Shin
      Jihye Shin
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      Advanced Medical Research Center, Yokohama City University, Kanazawa, Yokohama 236-0004, Japan
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    • Yumi Kwon
      Yumi Kwon
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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    • Seonjeong Lee
      Seonjeong Lee
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
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    • Seungjin Na
      Seungjin Na
      Department of Computer Science, Hanyang University, Seoul 04763, Korea
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    • Eun Young Hong
      Eun Young Hong
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
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      Shinyeong Ju
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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      Hyun-Gyo Jung
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
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    • Prashant Kaushal
      Prashant Kaushal
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
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    • Sungho Shin
      Sungho Shin
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
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    • Ji Hyun Back
      Ji Hyun Back
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
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    • Seon Young Choi
      Seon Young Choi
      Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
      Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul 06351, Korea
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      Eun Hee Kim
      Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul 06351, Korea
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      Su Jin Lee
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      Department of Life Science, College of Natural Sciences, Ewha Womans University, Seoul 03760, Korea
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    • Yae Eun Park
      Yae Eun Park
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
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      Hee-Sung Ahn
      Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea
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      Younghee Ahn
      Departments of Pediatrics, Clinical Neurosciences, Physiology & Pharmacology, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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      Won Suk Yang
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      Oh Young Bang
      Departments of Neurology, Samsung Medical Center, Sungkyunkwan University, Seoul 06351, Korea
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      Chul-Won Ha
      Department of Orthopedic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
      Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
      Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul 06351, Korea
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      Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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      Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 34113, Korea
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      Ji Eun Lee
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
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      Jin Young Kim
      Biomedical Omics Research Group, Korea Basic Research Institute, Ochang, Chungbuk 28119, Korea
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      Kwang Pyo Kim
      Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Gyeonggi 17104, Korea
      Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul 02453, Korea
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      Orcidhttp://orcid.org/0000-0003-0095-3787
    • Youngsoo Kim
      Youngsoo Kim
      Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul 03080, Korea
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      Hisashi Hirano
      Advanced Medical Research Center, Yokohama City University, Kanazawa, Yokohama 236-0004, Japan
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      Eugene C. Yi
      Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 03080, Korea
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      Je-Yoel Cho
      Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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      Eunok Paek
      Department of Computer Science, Hanyang University, Seoul 04763, Korea
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      Orcidhttp://orcid.org/0000-0003-3655-9749
    • Cheolju Lee*
      Cheolju Lee
      Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
      Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
      KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
      *E-mail: [email protected]
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      Orcidhttp://orcid.org/0000-0001-8482-4696
    Other Access OptionsSupporting Information (6)

    Journal of Proteome Research

    Cite this: J. Proteome Res. 2019, 18, 10, 3800–3806
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jproteome.9b00475
    Published September 2, 2019
    Copyright © 2019 American Chemical Society
    Request reuse permissions

    Abstract

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    We propose to use cRFP (common Repository of FBS Proteins) in the MS (mass spectrometry) raw data search of cell secretomes. cRFP is a small supplementary sequence list of highly abundant fetal bovine serum proteins added to the reference database in use. The aim behind using cRFP is to prevent the contaminant FBS proteins from being misidentified as other proteins in the reference database, just as we would use cRAP (common Repository of Adventitious Proteins) to prevent contaminant proteins present either by accident or through unavoidable contacts from being misidentified as other proteins. We expect it to be widely used in experiments where the proteins are obtained from serum-free media after thorough washing of the cells, or from a complex media such as SILAC, or from extracellular vesicles directly.

    Copyright © 2019 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jproteome.9b00475.

    • Table S1: Proteins identified from extracellular vesicle using HoDB (XLSX)

    • Table S2: Proteins identified from extracellular vesicle using HcRDB (XLSX)

    • Table S3: PSMs identified from extracellular vesicle using HoDB (XLSX)

    • Table S4: PSMs identified from extracellular vesicle using HcRDB (XLSX)

    • Table S5: PSM lists of U87MG secretome searched against HoDB and HcRDB (XLSX)

    • A FASTA file of cRFP database in a plain text format (TXT)

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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2019, 18, 10, 3800–3806
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jproteome.9b00475
    Published September 2, 2019
    Copyright © 2019 American Chemical Society
    Request reuse permissions

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