Avoiding pitfalls in proteomics sample preparation

Abstract

The purpose of this chapter is to focus on areas that are often underestimated in their importance for optimized results in mass spectrometric analyses, namely sample preparation. While there is no doubt that the advancements in technology led us to where we are now - it is also clear that a deep understanding of appropriate sample preparation techniques can be key to success of a proteomics experiment. Equally, lack of such knowledge can be the source of avoidable, failed experiments. Here, we will share our experience and discuss common contaminants such as buffers, solubilization reagents and those contaminants that are introduced through the use of specific biological protocols. The chapter will outline how best to deal with these common problems in order to maximize the returns from a proteomics experiment. We will also briefly discuss the importance of liquid chromatography and mass spectrometry optimization as well as bioinformatics tools to increase the amount of information that can be retrieved from such experiments.

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