首页|How to use open-pFind in deep proteomics data analysis?—A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data

How to use open-pFind in deep proteomics data analysis?—A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data

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High-throughput proteomics based on mass spectrometry(MS)analysis has permeated biomedical sci-ence and propelled numerous research projects.pFind 3 is a database search engine for high-speed and in-depth proteomics data analysis.pFind 3 features a swift open search workflow that is adept at un-covering less obvious information such as unexpected modifications or mutations that would have gone unnoticed using a conventional data analysis pipeline.In this protocol,we provide step-by-step instructions to help users mastering various types of data analysis using pFind 3 in conjunction with pParse for data pre-processing and if needed,pQuant for quantitation.This streamlined pParse-pFind-pQuant workflow offers exceptional sensitivity,precision,and speed.It can be easily implemented in any laboratory in need of identifying peptides,proteins,or post-translational modifications,or of quantitation based on 15N-labeling,SILAC-labeling,or TMT/iTRAQ labeling.

Protein identificationMass spectrometrySearch engineOpen-pFindQuantitation

Guangcan Shao、Yong Cao、Zhenlin Chen、Chao Liu、Shangtong Li、Hao Chi、Meng-Qiu Dong

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School of Life Sciences,Peking University,Beijing 100871,China

National Institute of Biological Sciences,Beijing,Beijing 102206,China

Tsinghua Institute of Multidisciplinary Biomedical Research,Tsinghua University,Beijing 102206,China

Key Lab of Intelligent Information Processing of Chinese Academy of Sciences(CAS),University of CAS,Institute of Computing Technology,CAS,Beijing 100190,China

University of Chinese Academy of Sciences,Beijing 100049,China

Beijing Advanced Innovation Center for Big Data-Based Precision Medicine,School of Medicine and Engineering,Beihang University,Beijing 100191,China

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21675153

2021

生物物理学报
中国生物物理学会 中国科学院生物物理研究所

生物物理学报

影响因子：0.355
ISSN：1000-6737
年,卷(期)：2021.7(3)
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