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  

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

机构地区：[1]School of Life Sciences,Peking University,Beijing 100871,China [2]National Institute of Biological Sciences,Beijing,Beijing 102206,China [3]Tsinghua Institute of Multidisciplinary Biomedical Research,Tsinghua University,Beijing 102206,China [4]Key Lab of Intelligent Information Processing of Chinese Academy of Sciences(CAS),University of CAS,Institute of Computing Technology,CAS,Beijing 100190,China [5]University of Chinese Academy of Sciences,Beijing 100049,China [6]Beijing Advanced Innovation Center for Big Data-Based Precision Medicine,School of Medicine and Engineering,Beihang University,Beijing 100191,China

出　　处：《Biophysics Reports》2021年第3期207-226,共20页生物物理学报（英文版）

基　　金：the National Natural Science Foundation of China(grant 21675153 Detail);the Beijing Municipal Science and Technology Commission,and the Ministry of Science and Technology of China for research funding.

摘　　要：High-throughput proteomics based on mass spectrometry(MS)analysis has permeated biomedical science 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 uncovering 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.

关 键 词：Protein identification Mass spectrometry Search engine Open-pFind QUANTITATION 

分 类 号：Q503[生物学—生物化学]