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Abstract

Among the MS-based quantitative methods using stable isotope labelling, the Isotope-Coded Protein Label (ICPL) technique has emerged as a powerful tool to identify and relatively quantify thousands of proteins within complex protein mixtures. The ICPL_ESIQuant 3.0 software package is one of the key components of the ICPL-ESI workflow, covering data processing steps like LC-MS feature detection, ICPL doublet/triplet/quadruplet quantification as well as a merging step of LC-MS features and Mascot search results. As unique features, the software performs isotope pattern overlap corrections and utilizes additional chemical knowledge, e.g. the physico-chemical properties of the ICPL labels, to discard false positive isotope pattern, which significantly improves the quality of the final peptide and protein results. ICPL_ESIQuant is the first freeware tool on the market, which supports both the shotgun proteomics strategy using Data Dependent Acquisition (DDA) and the directed proteomics strategy using mass inclusion lists for precursor ion selection. ICPL_ESIQuant 3.0 (32 and 64 bit versions) can be downloaded from https://sourceforge.net/projects/icplquant/ files/