ArMone: a software suite specially designed for processing and analysis of phosphoproteome data.

The development of new phosphoproteomic technologies has led to a rapid increase in the number of phosphoprotein identifications. Managing and extracting valuable information from the phosphoproteome data sets and generating output information in user-friendly formats require special data management and process platform. Even though a few proteome pipelines have been developed, they are mainly designed for processing data set of unmodified peptide/protein identifications. Because of the different characteristics of phosphorylated peptides/proteins, these pipelines are inconvenient, sometimes inappropriate, to process the phosphoproteome data sets. In this study, a software suite named ArMone was specially designed for the management and analysis of phosphoproteome data. It can readily identify phosphopeptides with high reliability and high sensitivity, and can effectively pinpoint the most probable phosphorylation site. A few well-designed postvalidation process tools are also available to extract and export valuable information. ArMone is a stand-alone application with friendly graphic user interface. It can run on different operating systems and can process data sets obtained by most of the commonly used database search engines.