MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications

Mass
spectrometry (MS) has become the tool of choice for the large
scale identification and quantitation of proteins and their post-translational
modifications (PTMs). This development has been enabled by powerful
software packages for the automated analysis of MS data. While data
on PTMs of thousands of proteins can nowadays be readily obtained,
fully deciphering the complexity and combinatorics of modification
patterns even on a single protein often remains challenging. Moreover,
functional investigation of PTMs on a protein of interest requires
validation of the localization and the accurate quantitation of its
changes across several conditions, tasks that often still require
human evaluation. Software tools for large scale analyses are highly
efficient but are rarely conceived for interactive, in-depth exploration
of data on individual proteins. We here describe MsViz, a web-based
and interactive software tool that supports manual validation of PTMs
and their relative quantitation in small- and medium-size experiments.
The tool displays sequence coverage information, peptide-spectrum
matches, tandem MS spectra and extracted ion chromatograms through
a single, highly intuitive interface. We found that MsViz greatly
facilitates manual data inspection to validate PTM location and quantitate
modified species across multiple samples.