Difficult Proteins

The degree of protein diversity and dynamic range within organisms means that even the simplest proteome cannot be captured by any single extraction and separation step. New techniques have focused on major protein classes often under-represented in proteome analysis; low abundance, membrane, and alkaline proteins. The last decade has seen considerable technology development in fractionation tools aimed at complexity reduction in many forms. The key outcome of complexity reduction is that each fraction, or sub-proteome, can be studied in more detail, and proteins which would have remained undetected in a total extract are present in sufficient quantities. However, the tools available are fractionations, not amplifications, and like all mining for rare and difficult items, a large amount of starting material is often required. The key shortcomings of many proteome analysis techniques are now well documented. With this knowledge, the best modern proteomics ‘platform’ involves combining multiple protein extractions, gel and chromatographic separations, and multiple MS analysis methods.