Citation: ZHOU Yue, HUANG Min, LI Xiang, GUAN Feng. Performance Evaluation of Data-Independent Acquisition-based Quantitative Proteomics on Three Types of Orbitrap Mass Spectrometers[J]. Chinese Journal of Analytical Chemistry, ;2021, 49(5): 820-829. doi: 10.19756/j.issn.0253-3820.201540 shu

Performance Evaluation of Data-Independent Acquisition-based Quantitative Proteomics on Three Types of Orbitrap Mass Spectrometers

ZHOU Yue ¹ ,
HUANG Min ² ,
LI Xiang ³ ,
GUAN Feng ^1,3,,

1.
Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China;
2.
Themofisher Scientific, Shanghai 200120, China;
3.
College of Life Sciences, Northwest University, Xi'an 710069, China

Corresponding author: GUAN Feng, guanfeng@nwu.edu.cn
Received Date: 7 September 2020
Revised Date: 12 January 2021

Fund Project: Supported by the National Science and Technology Major Project of China (No.2018ZX10302205).

Data-independent acquisition (DIA)-based quantitative proteomics has been widely used in life science and clinical proteomics research. In this study, the quantitative performance of three most common Orbitrap mass spectrometers (Q Exactive Plus, Q Exative HF-X and Orbitrap Fusion Lumos) used in proteomics were compared. A corresponding DIA method was established for each mass spectrometer and three groups of samples including commercial Hela digested peptides as QC sample, high abundant proteins depleted plasma samples and mixture samples of plasma and yeast at fixed ratios were designed to evaluate the proteome coverage, quantitative reproducibility, accuracy and precision. In QC sample, 34000-37000 peptides and 4400 proteins were quantified by each mass spectrometer, 81% of the peptides and 96% of the proteins were quantified by all mass spectrometers, and the median coefficient of variations of protein intensities were below 5%. In depleted plasma samples, each mass spectrometer quantified 4400-5100 peptides and 550-620 proteins with a 60-min gradient, 64% of the peptides and 80% of the proteins were quantified by each mass spectrometer, and the median coefficient of variations of protein intensities were below 5%. In a mixed sample with known ratios, each mass spectrometer quantified 260-297 plasma proteins and 2210-2436 yeast proteins. The precision and number of differential proteins were comparable. Due to the difference in the hardware design of three mass spectrometers, quantification was affected by the batch effect when combined analysis was performed. After batch effect normalization, the quantitative performance was equivalent to that of each mass spectrometer. These results showed that the quantitative performance of DIA on three mass spectrometers was comparable and provided reference for large scale DIA quantification with multiple Orbitraps.
- Data-independent acquisition,
- Quantitative proteomics,
- Orbitrap mass spectrometer
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