Improving the performance of proteomic analysis via VAILase cleavage and 193-nm ultraviolet photodissociation

Binwen Sun; Zheyi Liu; Xiang Fang; Xiaolei Wang; Can Lai; Lin Liu; Chunlei Xiao; You Jiang; Fangjun Wang

doi:10.1016/j.aca.2021.338340

Improving the performance of proteomic analysis via VAILase cleavage and 193-nm ultraviolet photodissociation

Anal Chim Acta. 2021 Apr 22:1155:338340. doi: 10.1016/j.aca.2021.338340. Epub 2021 Feb 20.

Authors

Binwen Sun¹, Zheyi Liu², Xiang Fang³, Xiaolei Wang⁴, Can Lai¹, Lin Liu⁵, Chunlei Xiao⁶, You Jiang⁷, Fangjun Wang⁸

Affiliations

¹ CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
² CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
³ National Institute of Metrology, Beijing, 100013, China.
⁴ CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian, 116023, China.
⁵ School of Life Sciences, Anhui University, 230601, Hefei, Anhui, China.
⁶ State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian, 116023, China. Electronic address: chunleixiao@dicp.ac.cn.
⁷ National Institute of Metrology, Beijing, 100013, China. Electronic address: jiangyou@nim.ac.cn.
⁸ CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China. Electronic address: wangfj@dicp.ac.cn.

PMID: 33766312
DOI: 10.1016/j.aca.2021.338340

Abstract

Further improving the proteomic identification coverage and reliability is still challenging in the mass spectrometry (MS)-based proteomics. Herein, we combine VAILase and trypsin digestion with 193-nm ultraviolet photodissociation (UVPD) and higher-energy collision dissociation (HCD) to improve the performance of bottom-up proteomics. As VAILase exhibits high complementarity to trypsin, the proteome sequence coverage is improved obviously whether with HCD or 193-nm UVPD. The high diversity of fragment ion types produced by UVPD contributes to the improvements of identification reliability for both trypsin- and VAILase-digested peptides with an average XCorr score improvement of 10%.

Keywords: Bottom-up proteomics strategy; Mass spectrometry; Protease; Ultraviolet photodissociation.

MeSH terms

Peptides
Proteomics*
Reproducibility of Results
Tandem Mass Spectrometry*
Ultraviolet Rays

Substances

Peptides