Introduction

IsobaricQuant, a Java-based software tool for the quantification, visualization, and filtering of isobarically-labeled peptides. IsobaricQuant is a cross-platform standalone tool that can be operated via an intuitive graphical user interface (GUI), or integrated into custom pipelines via command line.

For input, it requires the mzML file of the MS run, a CSV file containing peptide spectral matches (PSM) obtained from a search engine, and a user-supplied text configuration file. Optionally, isotopic impurity correction can be performed using a reporter ion isotopic distribution CSV file. IsobaricQuant supports MS2 and MS3 level reporter ion quantification for iTRAQ up to 8-plex, TMT up to 11-plex and TMTpro up to 16-plex.

An integrated viewer allows visual inspection of isolation window purity in MS1 scans, reporter ion quantification, and fragment ion assignment. For MS3 acquisition methods, it further enables visual assessment of SPS ion selection.