Bioinformatics Tools for Mass Spectrometry-based Proteomics Analysis

In recent years mass spectrometry-based proteomics became very important and now it is the leading approach employed in high-throughput analysis. Its relevance increased thanks to availability of genome-sequence database and the development of high sensitivity instruments allows a rapid and automated proteins profiling. The need to analyze complex biological samples at a large-scale level required the development of computational tools to analyze and statistically evaluate data generated from mass spectrometry (MS) experiments. These aspects have stimulated the young emerging field of bioinformatics in proteomics to introduce new software and algorithms to handle large and heterogeneous data sets and to improve the knowledge of discovery process. This review discusses of the most recent progresses in bioinformatics tools useful in mass spectrometry-based proteomics. In particular we will be focusing on software applications applied to proteomics profiling biomarker discovery and cluster analysis. Finally since most known mechanisms leading to biological processes involve different molecules here are reported the most recent methodologies to investigate biological systems through their underlying interactions with particular attention to protein-protein interaction.