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Accurate Proteoform Identification and Quantitation Using pTop 2.0

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Proteoform Identification

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2500))

Abstract

The remarkable advancement of top-down proteomics in the past decade is driven by the technological development in separation, mass spectrometry (MS) instrumentation, novel fragmentation, and bioinformatics. However, the accurate identification and quantification of proteoforms, all clearly-defined molecular forms of protein products from a single gene, remain a challenging computational task. This is in part due to the complicated mass spectra from intact proteoforms when compared to those from the digested peptides. Herein, pTop 2.0 is developed to fill in the gap between the large-scale complex top-down MS data and the shortage of high-accuracy bioinformatic tools. Compared with pTop 1.0, the first version, pTop 2.0 concentrates mainly on the identification of the proteoforms with unexpected modifications or a terminal truncation. The quantitation based on isotopic labeling is also a new function, which can be carried out by the convenient and user-friendly “one-key operation,” integrated together with the qualitative identifications. The accuracy and running speed of pTop 2.0 is significantly improved on the test data sets. This chapter will introduce the main features, step-by-step running operations, and algorithmic developments of pTop 2.0 in order to push the identification and quantitation of intact proteoforms to a higher-accuracy level in top-down proteomics.

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Acknowledgments

This research was supported by the National Natural Science Foundation of China (No. 31670837). The authors thank Hao Yang, Wen-Jing Zhou, Xiao-Jin Zhang, and Zhao-Wei Wang from the Institute of Computing Technology; Zhe-Yi Liu and Fang-Jun Wang from Dalian Institute of Chemical Physics, Chinese Academy of Sciences; and Yong Cao and Meng-Qiu Dong from National Institute of Biological Sciences, Beijing, for MS Data acquisition and valuable discussions to improve this chapter.

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Authors and Affiliations

  1. National Institute of Biological Sciences, Beijing, China

    Rui-Xiang Sun

  2. Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China

    Rui-Xiang Sun, Rui-Min Wang, Lan Luo, Chao Liu, Hao Chi, Wen-Feng Zeng & Si-Min He

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  1. Rui-Xiang Sun
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  2. Rui-Min Wang
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  3. Lan Luo
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  4. Chao Liu
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  5. Hao Chi
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  6. Wen-Feng Zeng
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  7. Si-Min He
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Correspondence to Rui-Xiang Sun .

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Editors and Affiliations

  1. Department of Chemistry, Michigan State University, East Lansing, MI, USA

    Liangliang Sun

  2. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA

    Xiaowen Liu

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Sun, RX. et al. (2022). Accurate Proteoform Identification and Quantitation Using pTop 2.0. In: Sun, L., Liu, X. (eds) Proteoform Identification. Methods in Molecular Biology, vol 2500. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2325-1_9

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  • DOI: https://doi.org/10.1007/978-1-0716-2325-1_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2324-4

  • Online ISBN: 978-1-0716-2325-1

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