Mass Spectrometry-Based Protein Quantification
Quantification of individual proteins and even entire proteomes is an important theme in proteomics research. Quantitative proteomics is an approach to obtain quantitative information about proteins in a sample. Compared to qualitative or semi-quantitativ
- PDF / 1,048,220 Bytes
- 25 Pages / 504.567 x 720 pts Page_size
- 98 Downloads / 189 Views
15
Yun Chen, Fuqiang Wang, Feifei Xu, and Ting Yang
Abstract
Quantification of individual proteins and even entire proteomes is an important theme in proteomics research. Quantitative proteomics is an approach to obtain quantitative information about proteins in a sample. Compared to qualitative or semi-quantitative proteomics, this approach can provide more insight into the effects of a specific stimulus, such as a change in the expression level of a protein and its posttranslational modifications, or to a panel of proposed biomarkers in a given disease state. Proteomics methodologies, along with a variety of bioinformatics approaches, are a major tool in quantitative proteomics. As the theory and technological aspects underlying the proteomics methodologies will be extensively described in Chap. 20, and protein identification as a prerequisite of quantification has been discussed in Chap. 17, we will focus on the quantitative proteomics bioinformatics algorithms and software tools in this chapter. Our goal is to provide researchers and newcomers a rational framework to select suitable bioinformatics tools for data analysis, interpretation, and integration in protein quantification. Before doing so, a brief overview of quantitative proteomics is provided. Keywords
Protein quantification bioinformatics • Quantitative signal processing • SAPRatio • MAXquant • Progenesis QI • APEX • Trans-Proteomic Pipeline (TPP) • IsobariQ and Iquant • Targeted proteomics • PeptideAtlas • Skyline • ATAQS
15.1 Y. Chen (*) • F. Wang • F. Xu • T. Yang School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing 211166, China e-mail: [email protected]
Brief Introduction of Quantitative Proteomics
Despite a number of recent developments in proteomics-associated technologies, such as
# Springer International Publishing Switzerland 2016 H. Mirzaei and M. Carrasco (eds.), Modern Proteomics – Sample Preparation, Analysis and Practical Applications, Advances in Experimental Medicine and Biology 919, DOI 10.1007/978-3-319-41448-5_15
255
256
two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and protein microarrays [1], mass spectrometry (MS)-based proteomics remains an essential technique for quantitative proteome analyses. Our focus here is on MS-based proteomics. In MS-based proteomics, two fundamental approaches are currently employed: top-down and bottom-up proteomics. In top-down proteomics, intact proteins or large fragments are subjected to mass spectrometry. Bottom-up proteomics relies on proteolytic peptides, which are generated by enzymatic digestion of proteins. Of several such strategies that have been developed, all involve the digestion of proteins into peptides, typically with trypsin, followed by chromatographic separation, ionization and mass spectrometric analysis of the complex peptide samples. Due to the protein size limitation (
Data Loading...
