title: Mass Spectrometry-Based Protein Quantification.
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.
authors.affiliation: School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing, 211166, China. ychen@njmu.edu.
authors.forename: Yun
authors.initials: Y
authors.lastname: Chen
authors.affiliation: School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing, 211166, China.
authors.forename: Fuqiang
authors.initials: F
authors.lastname: Wang
authors.affiliation: School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing, 211166, China.
authors.forename: Feifei
authors.initials: F
authors.lastname: Xu
authors.affiliation: School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing, 211166, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D000818:Animals; D015415:Biomarkers / Q000032:analysis; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D057166:High-Throughput Screening Assays; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis*; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D015415:Biomarkers; D011506:Proteins; D020543:Proteome
keywords: APEX; ATAQS; IsobariQ and Iquant; MAXquant; PeptideAtlas; Progenesis QI; Protein quantification bioinformatics; Quantitative signal processing; SAPRatio; Skyline; Targeted proteomics; Trans-Proteomic Pipeline (TPP)