Common Repository of FBS Proteins (cRFP) To Be Added to a Search Database for Mass Spectrometric Analysis of Cell Secretome

Jihye Shin; Yumi Kwon; Seonjeong Lee; Seungjin Na; Eun Young Hong; Shinyeong Ju; Hyun-Gyo Jung; Prashant Kaushal; Sungho Shin; Ji Hyun Back; Seon Young Choi; Eun Hee Kim; Su Jin Lee; Yae Eun Park; Hee-Sung Ahn; Younghee Ahn; Mohammad Humayun Kabir; Seong-Jun Park; Won Suk Yang; Jeonghun Yeom; Oh Young Bang; Chul-Won Ha; Jin-Won Lee; Un-Beom Kang; Hye-Jung Kim; Kang-Sik Park; J Eugene Lee; Ji Eun Lee; Jin Young Kim; Kwang Pyo Kim; Youngsoo Kim; Hisashi Hirano; Eugene C Yi; Je-Yoel Cho; Eunok Paek; Cheolju Lee

doi:10.1021/acs.jproteome.9b00475

Common Repository of FBS Proteins (cRFP) To Be Added to a Search Database for Mass Spectrometric Analysis of Cell Secretome

J Proteome Res. 2019 Oct 4;18(10):3800-3806. doi: 10.1021/acs.jproteome.9b00475. Epub 2019 Sep 10.

Authors

Jihye Shin^{1

2}, Yumi Kwon^{1

3}, Seonjeong Lee^{1

4}, Seungjin Na⁵, Eun Young Hong¹, Shinyeong Ju^{1

3}, Hyun-Gyo Jung^{1

4}, Prashant Kaushal^{1

4}, Sungho Shin^{1

6}, Ji Hyun Back^{1

7}, Seon Young Choi^{8

9}, Eun Hee Kim⁹, Su Jin Lee^{1

10}, Yae Eun Park^{1

11}, Hee-Sung Ahn¹², Younghee Ahn¹³, Mohammad Humayun Kabir¹⁴, Seong-Jun Park¹⁵, Won Suk Yang¹⁶, Jeonghun Yeom¹⁷, Oh Young Bang¹⁸, Chul-Won Ha^{8

9

19}, Jin-Won Lee³, Un-Beom Kang²⁰, Hye-Jung Kim²¹, Kang-Sik Park^{6

22}, J Eugene Lee²³, Ji Eun Lee¹, Jin Young Kim²⁴, Kwang Pyo Kim^{25

26}, Youngsoo Kim²⁷, Hisashi Hirano², Eugene C Yi²⁸, Je-Yoel Cho²⁹, Eunok Paek⁵, Cheolju Lee^{1

4

6}

Affiliations

¹ Center for Theragnosis, Korea Institute of Science and Technology , Seoul 02792 , Korea.
² Advanced Medical Research Center , Yokohama City University , Kanazawa , Yokohama 236-0004 , Japan.
³ Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea.
⁴ Division of Bio-Medical Science & Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea.
⁵ Department of Computer Science , Hanyang University , Seoul 04763 , Korea.
⁶ KHU-KIST Department of Converging Science and Technology , Kyung Hee University , Seoul 02447 , Korea.
⁷ Department of Biotechnology, College of Life Sciences and Biotechnology , Korea University , Seoul 02841 , Korea.
⁸ Department of Health Sciences and Technology, SAIHST , Sungkyunkwan University , Seoul 06351 , Korea.
⁹ Stem Cell & Regenerative Medicine Institute , Samsung Medical Center , Seoul 06351 , Korea.
¹⁰ Department of Life Science, College of Natural Sciences , Ewha Womans University , Seoul 03760 , Korea.
¹¹ Department of Biochemistry, College of Life Science and Biotechnology , Yonsei University , Seoul 03722 , Korea.
¹² Asan Institute for Life Sciences , Asan Medical Center , Seoul 05505 , Korea.
¹³ 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.
¹⁴ Incepta Vaccine Limited , Dhamrai , Kalampur 1351 , Dhaka , Bangladesh.
¹⁵ RetiMark Co. Ltd. , Seoul 04385 , Korea.
¹⁶ R&D Center for Clinical Mass Spectrometry , Seegene Medical Foundation , Seoul 04805 , Korea.
¹⁷ Toxicological Laboratory, Department of Emergency Medicine , Asan Medical Center , Seoul 05505 , Korea.
¹⁸ Departments of Neurology, Samsung Medical Center , Sungkyunkwan University , Seoul 06351 , Korea.
¹⁹ Department of Orthopedic Surgery, Samsung Medical Center , Sungkyunkwan University School of Medicine , Seoul 06351 , Korea.
²⁰ Core Protein Resources Center , Daegu Gyeongbuk Institute of Science and Technology , Daegu 42988 , Korea.
²¹ New Drug Development Center , KBIO Osong Medical Innovation Foundation , Cheongju-si , Chungbuk 28160 , Korea.
²² Department of Physiology, School of Medicine , Kyung Hee Univeristy , Seoul 02447 , Korea.
²³ Center for Bioanalysis , Korea Research Institute of Standards and Science , Daejeon 34113 , Korea.
²⁴ Biomedical Omics Research Group , Korea Basic Research Institute , Ochang , Chungbuk 28119 , Korea.
²⁵ Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials , Kyung Hee University , Yongin , Gyeonggi 17104 , Korea.
²⁶ Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute , Kyung Hee University , Seoul 02453 , Korea.
²⁷ Department of Biomedical Engineering , Seoul National University College of Medicine , Seoul 03080 , Korea.
²⁸ Department of Molecular Medicine and Biopharmaceutical Sciences , Seoul National University , Seoul 03080 , Korea.
²⁹ Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine , Seoul National University , Seoul 08826 , Korea.

PMID: 31475827
DOI: 10.1021/acs.jproteome.9b00475

Abstract

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.

Keywords: common repository of FBS proteins; database search; secretome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cattle
Cells, Cultured / metabolism*
Culture Media / chemistry
Databases, Protein
Humans
Mass Spectrometry
Proteome / analysis*
Proteomics / methods*
Serum / chemistry*

Substances

Culture Media
Proteome