A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology

Yi Di; Wenxue Li; Barbora Salovska; Qian Ba; Zhenyi Hu; Shisheng Wang; Yansheng Liu

doi:10.52601/bpr.2023.230007

Volume 9 Issue 2

Apr. 2023

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Article Navigation > Biophysics Reports > 2023 > 9(2): 82-98

Yi Di, Wenxue Li, Barbora Salovska, Qian Ba, Zhenyi Hu, Shisheng Wang, Yansheng Liu. A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. Biophysics Reports, 2023, 9(2): 82-98. doi: 10.52601/bpr.2023.230007

Citation:

Yi Di, Wenxue Li, Barbora Salovska, Qian Ba, Zhenyi Hu, Shisheng Wang, Yansheng Liu. A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. Biophysics Reports, 2023, 9(2): 82-98. doi: 10.52601/bpr.2023.230007

Citation:

Yi Di, Wenxue Li, Barbora Salovska, Qian Ba, Zhenyi Hu, Shisheng Wang, Yansheng Liu. A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. Biophysics Reports, 2023, 9(2): 82-98. doi: 10.52601/bpr.2023.230007

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A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology

doi: 10.52601/bpr.2023.230007

Yi Di^{1, Y},
Wenxue Li^{1, Y},
Barbora Salovska^{1, Y},
Qian Ba^{1, 2},
Zhenyi Hu¹,
Shisheng Wang³,
Yansheng Liu^{1, 4
,
,}

1.
Cancer Biology Institute, Yale University School of Medicine, West Haven, CT 06516, USA
2.
Current address: Laboratory Center, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, China
3.
Department of Pulmonary and Critical Care Medicine, and Proteomics-Metabolomics Analysis Platform, West China Hospital, Sichuan University, Chengdu 610041, China
4.
Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA

More Information

Corresponding author: yansheng.liu@yale.edu
Received Date: 09 April 2023
Accepted Date: 28 April 2023

Available Online: 31 August 2023

Publish Date: 01 April 2023

Abstract

Abstract

Phosphorylation is one of the most important post-translational modifications (PTMs) of proteins, governing critical protein functions. Most human proteins have been shown to undergo phosphorylation, and phosphoproteomic studies have been widely applied due to recent advancements in high-resolution mass spectrometry technology. Although the experimental workflow for phosphoproteomics has been well-established, it would be useful to optimize and summarize a detailed, feasible protocol that combines phosphoproteomics and data-independent acquisition (DIA), along with follow-up data analysis procedures due to the recent instrumental and bioinformatic advances in measuring and understanding tens of thousands of site-specific phosphorylation events in a single experiment. Here, we describe an optimized Phos-DIA protocol, from sample preparation to bioinformatic analysis, along with practical considerations and experimental configurations for each step. The protocol is designed to be robust and applicable for both small-scale phosphoproteomic analysis and large-scale quantification of hundreds of samples for studies in systems biology and systems medicine.
- Bioinformatic analysis,
- High-resolution mass spectrometry technology,
- Phosphoproteomics,
- Systems biology,
- Systems medicine

Yi Di, Wenxue Li, Barbora Salovska, Qian Ba, Zhenyi Hu, Shisheng Wang and Yansheng Liu declare that they have no conflict of interests.
This article does not contain any studies with human or animal subjects performed by any of the authors.
Yi Di, Wenxue Li and Barbora Salovaska contributed equally to this work and are listed based on alphabetic order.

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References(62)

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