Protein identification and profiling with mass spectrometry

As a consequence of the completion of multiple genome projects, there has emerged a need for the efficient evaluation of complex samples of proteins on a broad scale [1–4]. Mass spectrometry (MS) has rapidly become one of the most important tools for the identification of proteins (Fig. 1) largely due to the introduction of new biomolecule-compatible ionization techniques such as electrospray ionization (ESI) [5] and matrix-assisted laser desorption/ionization (MALDI) [6] as well as high resolution mass analyzers. Using these technologies, proteolytic peptides can be ionized intact into the gas phase and their masses accurately measured. Based on this information, proteins can readily be identified using a methodology called protein mass mapping or peptide mass mapping, in which these measured masses are compared to predicted values derived from a protein database. Further sequence information can also be obtained by fragmenting individual peptides in tandem MS experiments. In addition, large scale changes in protein expression levels between two different samples can be assessed using quantitative tools such as two-dimensional gel electrophoresis (2D-GE) or staple isotope labeling in conjunction with mass spectrometry measurement.