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

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

doi:10.52601/bpr.2021.210004

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

Biophys Rep. 2021 Jun 30;7(3):207-226. doi: 10.52601/bpr.2021.210004.

Authors

Guangcan Shao^{1

2

3}, Yong Cao^{1

2

3}, Zhenlin Chen^{4

5}, Chao Liu^{4

6}, Shangtong Li^{2

3}, Hao Chi⁴, Meng-Qiu Dong^{2

3}

Affiliations

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.

Abstract

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.

Keywords: Mass spectrometry; Open-pFind; Protein identification; Quantitation; Search engine.