Proteomics

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Common Repository of FBS Proteins (cRFP) to be added to a search database for mass spectrometric analysis of cell secretome


ABSTRACT: We propose to use cRFP (common Repository of FBS Proteins) in the MS (mass spectrometry) raw data search of cell secretome. cRFP is a small supplementary sequence list of high 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.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

SUBMITTER: Yumi Kwon  

LAB HEAD: Cheolju Lee

PROVIDER: PXD015143 | Pride | 2019-09-04

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
160210_exo_4th_3_mock_01.RAW Raw
160210_exo_4th_3_mock_02.RAW Raw
160210_exo_4th_3_mock_03.RAW Raw
160210_exo_4th_3_mock_04.RAW Raw
Exo_HcRDB.msf Msf
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Publications

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

Shin Jihye J   Kwon Yumi Y   Lee Seonjeong S   Na Seungjin S   Hong Eun Young EY   Ju Shinyeong S   Jung Hyun-Gyo HG   Kaushal Prashant P   Shin Sungho S   Back Ji Hyun JH   Choi Seon Young SY   Kim Eun Hee EH   Lee Su Jin SJ   Park Yae Eun YE   Ahn Hee-Sung HS   Ahn Younghee Y   Kabir Mohammad Humayun MH   Park Seong-Jun SJ   Yang Won Suk WS   Yeom Jeonghun J   Bang Oh Young OY   Ha Chul-Won CW   Lee Jin-Won JW   Kang Un-Beom UB   Kim Hye-Jung HJ   Park Kang-Sik KS   Lee J Eugene JE   Lee Ji Eun JE   Kim Jin Young JY   Kim Kwang Pyo KP   Kim Youngsoo Y   Hirano Hisashi H   Yi Eugene C EC   Cho Je-Yoel JY   Paek Eunok E   Lee Cheolju C  

Journal of proteome research 20190910 10


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 pr  ...[more]

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