Chapter 8: Bioinformatics for Qualitative and Quantitative Proteomics

Proteomics is the large-scale study of entire proteins. As a complementary approach to genomics and transcriptomics, it can provide comprehensive and direct information in exploring biological process. Mass Spectrometry (MS)- based technologies are the main approaches in modern proteomics studies. Protein identification and quantification are two major tasks in proteomics study, which could advance our understanding of the complex and dynamic nature of proteins. Proteomics studies have been widely applied in biological and clinical fields in identifying biomarkers, monitoring disease status, and assessing treatment effect. However, researchers have to face a pressing problem that how to deal with the high-throughput data generated form MS-based proteomics platform. In this chapter, we will introduce some bioinformatics databases and tools which are widely used in protein identification and quantification, proteomics data analysis, storage and sharing.