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

Volume 7 Issue 3

Jun. 2021

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Article Navigation > Biophysics Reports > 2021 > 7(3): 207-226

Guangcan Shao, Yong Cao, Zhenlin Chen, Chao Liu, Shangtong Li, Hao Chi, Meng-Qiu Dong. 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[J]. Biophysics Reports, 2021, 7(3): 207-226. doi: 10.52601/bpr.2021.210004

Citation:

Guangcan Shao, Yong Cao, Zhenlin Chen, Chao Liu, Shangtong Li, Hao Chi, Meng-Qiu Dong. 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[J]. Biophysics Reports, 2021, 7(3): 207-226. doi: 10.52601/bpr.2021.210004

Citation:

Guangcan Shao, Yong Cao, Zhenlin Chen, Chao Liu, Shangtong Li, Hao Chi, Meng-Qiu Dong. 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[J]. Biophysics Reports, 2021, 7(3): 207-226. doi: 10.52601/bpr.2021.210004

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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

doi: 10.52601/bpr.2021.210004

Guangcan Shao^{1, 2, 3},
Yong Cao^{1, 2, 3
,
,},
Zhenlin Chen^{4, 5},
Chao Liu^{4, 6},
Shangtong Li^{2, 3},
Hao Chi^{4
,
,},
Meng-Qiu Dong^{2, 3
,
,}

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

Funds: The authors would like to thank Yong-Hong Yan, Dr. Li Tao, and Yue Zhao of NIBS, Beijing and Dr. Ming Ding of China Pharmaceutical University for providing sample datasets to this protocol. The authors also thank the National Natural Science Foundation of China (grant 21675153), the Beijing Municipal Science and Technology Commission, and the Ministry of Science and Technology of China for research funding.

More Information

Corresponding author: caoyong@nibs.ac.cn (Y. Cao); chihao@ict.ac.cn (H. Chi); dongmengqiu@nibs.ac.cn (M.-Q. Dong)
Received Date: 07 February 2021
Accepted Date: 05 April 2021

Available Online: 07 July 2021

Publish Date: 30 June 2021

Abstract

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.
- Protein identification,
- Mass spectrometry,
- Search engine,
- Open-pFind,
- Quantitation

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References(15)

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