ESIQuant – a Powerful Freeware Tool for Handling Proteomics LC-ESI-MS 2 Experiments

By using the Isotope-Coded Protein Label (ICPL) approach [1,2] up to four different proteomics states can be compared with regard to their relative protein amounts. Measuring the samples using Liquid Chromatography coupled to Mass Spectrometry (LC-MS) results in hundreds and thousands of MS signals, each comprising m/z, intensity and retention time information of a certain compound ion. In order to detect and quantify peptides and proteins, many different software tools have been developed in the recent years, most of them comprising very intelligent peak picking and deisotoping algorithms [3].