Introduction

DeCyder™ MS Differential Analysis Software (DeCyder MS) is a new tool for visualization, detection, identification and label-free relative quantification of LC-MS and LC-MS/MS data. To Assess its quantification abilities, in a complex background, total soluble trypsin digested proteins extracts from strains of E.coli expressing varying levels of dihydrofolate reducatase (DHFR) were analysed using nanoLC-MS/MS. Full scan MS spectra were matched and quantified using DeCyder MS. A second experiment was performed on a bacterial strain containing an inducible integrase.