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Software Development for Quantitative Proteomics Using Stable Isotope Labeling

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Bioinformatics of Human Proteomics

Part of the book series: Translational Bioinformatics ((TRBIO,volume 3))

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Abstract

Stable isotope labeling (SIL) coupled with liquid chromatography and high-resolution tandem mass spectrometry (MS) are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Developments of more effective programs for the relative peptide/protein abundance measurements are essential for quantitative proteomic analysis. In this chapter, we present a quantification program, termed UNiquant, for analyzing quantitative proteomic data using SIL. The common steps in a quantitative proteomic software, such as MS data preprocessing, peptide identification, peptide quantification, and protein quantification, were dissected in this chapter, using UNiquant as an example. UNiquant was used to analyze the SILAC-labeled proteome mixtures with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10). The pros and cons of the quantification results of UNiquant from two different MS acquisition modes, data-dependent acquisition and data-independent acquisition, were also evaluated and compared.

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Author information

Authors and Affiliations

  1. Department of Pathology and Microbiology, University of Nebraska Medical Centre, Omaha, NE, USA

    Xin Huang Ph.D. & Shi-Jian Ding Ph.D.

  2. Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, NE, USA

    Shi-Jian Ding Ph.D.

Authors
  1. Xin Huang Ph.D.
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  2. Shi-Jian Ding Ph.D.
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Correspondence to Shi-Jian Ding Ph.D. .

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Editors and Affiliations

  1. , Medicine, Biomedical Research Center, Fudan University Zhongshan Hospital, Shang Hai, China, People's Republic

    Xiangdong Wang

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Huang, X., Ding, SJ. (2013). Software Development for Quantitative Proteomics Using Stable Isotope Labeling. In: Wang, X. (eds) Bioinformatics of Human Proteomics. Translational Bioinformatics, vol 3. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5811-7_12

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