Evaluation of Proteomic Data: From Profiling to Network Analysis by Way of Biomarker Discovery

Mass spectrometry coupled to liquid-chromatography (LC-MS) has emerged as the core tool for large-scale proteomic analysis. Current proteomic methodologies based on LC-MS may be grouped in two categories: shotgun and targeted proteomics for discovery and validation purposes, respectively. Nowadays, one of the most interesting and exciting applications of MS concerns proteomic analysis. The introduction of soft ionization methods, such as MALDI (matrix-assisted laser ionization desorption) and ESI (electrospray ionization), was one of the major turning points in MS-based proteomic studies. Shotgun proteomics have demonstrated, over the years, a great capability to characterize hundreds/thousands of proteins per sample, delivering a good representation of the analyzed complex biological systems. In the last years, systems biology has provided powerful strategies for linking protein profiles and biomarkers with biological processes that can be segmented and linked to disease presentation.