Bioinformatics for mass spectrometry-based proteomics

In recent years, there have been significant advancements in informatics supporting mass spectrometry-based proteomics research, including the development of a wide array of open-source and commercial tools for processing mass spectrometry data. While the processes are established for many commonly studied organisms, the study of HIV-1 and other viruses can be more challenging. Success requires a clear understanding of existing information in public protein databases, whether a custom protein sequence database is required, and which particular features of the bioinformatics platform are essential for HIV-1 proteomics. This chapter provides an introduction to the framework required for proteomic analyses and highlights current challenges involved with informatics surrounding HIV-1 proteomics. Readers are first introduced to the types of data that are generated in a mass spectrometry-based proteomics experiment and then how these data are analyzed. For each step in the workflow, important considerations and opportunities for data quality improvement are highlighted. The chapter concludes with a view on the future of systems biology studies using HIV-1 proteomics. Although the potential for these emerging technologies is just beginning to be explored, this chapter aims to illustrate how integration of bioinformatics and proteomic technologies, along with coordination among proteomic scientists, virologists, and clinicians, is poised to make significant contributions to the future of HIV-1 biology.