From protein redistribution to peptide detectability: Applications and developments of tandem mass spectrometry.

摘要

Approaches combining mass spectrometry (MS) based proteomics with classic cell biology techniques play an important role in advancing our understanding of cell biology. MS technology/method developments are often driven by biological questions, and when developed, can drive new biological insights. In this body of work the case study of protein redistribution highlights the importance of the cell's ability to shift the subcellular localizations of proteins in response to changes in the cellular environment. This finding raised many exciting questions such as which proteins redistribute, how many proteins redistribute, and how we can measure protein redistribution in a high-throughput manner. These questions demanded that we develop a new strategy combining a new MS method with subcellular fractionation, which was used in order to achieve analysis of an almost complete proteome of S. cerevisiae by overcoming the limitations of the current MS platforms. Another application using the novel data-sets acquired from yeast was the study of the physicochemical properties of orphan peptides, which provided novel insights into peptide detectability derived from the new MS method. Finally, a strategy combining principles of classic subcellular fractionation with quantitative proteomic analysis was developed to measure condition-specific protein redistribution on a global scale which enabled us to investigate the interesting questions that were previously not feasible in terms of simplicity and reproducibility.