ICPL_ESIQuant

ICPL_ESIQuant is a proteomics software tool designed to quantitatively analyze extensive mass spectrometric datasets derived from ICPL-based proteomics experiments. This tool can process mass spectrometric data from different equipment manufacturers and employs results from the Mascot search engine to generate protein and peptide outcome tables. The software is introduced here, along with a comprehensive tutorial outlining step-by-step instructions for its utilization with mass spectrometry datasets obtained from ICPL duplex, triplex, and quadruplex experiments. It necessitates input in the form of MS raw data saved in .mzXML file format and Mascot search results in .dat format. ICPL_ESIQuant is proficient in quantifying ICPL-labeled proteins and furnishes supplementary insights into all identified features in the sample, including those that were sequenced and detected. The tool accommodates both shotgun and directed proteomics approaches, allowing users to employ mass inclusion lists for identifying peptides that were not fragmented in the initial MS cycle.