Protein Identification and Quantification by Mass Spectrometry-Based Analysis: Applications in Plant-Pathogen Interactions Studies

Mass spectrometry (MS) has become an essential technology for proteomics applications in biological sciences. Advances in this technique have been possible owing to improvements in MS instrumentation, new experimental strategies in sample preparation, and development of bioinformatics tools for data analyses. In recent years, complementary strategies to the classical two-dimensional gel electrophoresis approaches (2-DE) have been developed. These techniques are based on multidimensional peptide separation coupled to tandem MS (also referred as “second generation proteomics”), enabling protein expression analysis and high throughput protein identification studies. New methods such as Multidimensional Protein Identification Technology (MudPIT) and stable isotope labeling of protein/peptide samples (either by chemical, metabolic, or enzymatic methods), among others, are powerful tools for large-scale studies on characterization and expression of proteins in complex biological systems. Hence, these techniques can be very useful in the study of plant-pathogen interactions, aiding to detect and characterize both plant proteins concerned in defense reactions and pathogen proteins involved in pathogenicity and/or virulence. But these techniques have been implemented in these biological systems just recently. We will examine here how MS-based proteomics approaches are helping to better understand the multifaceted phenomena underlying plant-pathogen interactions.