Analytical methods for proteome data obtained from SDS-PAGE multi-dimensional separation and mass spectrometry

For proteome analysis, various experimental protocols using mass spectrometry have been developed over the last decade. The different protocols have differing performances and degrees of accuracy. Furthermore, the “best” protocol for a proteomic analysis of a sample depends on the purpose of the analysis, especially in connection with disease proteomics, including biomarker discovery and therapeutics analyses of human serum or plasma. The protein complexity and the wide dynamic range of blood samples require high-dimensional separation technology. In this article, we review proteome analysis protocols in which both Sodium Dodecyl Sulfate-Polyacryl Amide Gel Electrophoresis(SDS-PAGE) and liquid chromatography are used for peptide and protein separations. Multidimensional separation technology supplies a high-quality dataset of tandem mass spectra and reveals signals from low-abundance proteins, although it can be time-consuming and laborious work. We survey shotgun proteomics protocols using SDS-PAGE and liquid chromatography and introduce bioinformatics tools for the analysis of proteomics data. We also review efforts toward the biological interpretation of the proteome.