Spectronaut A fast and efficient algorithm for MRM-like processing of data independent acquisition (SWATH-MS) data

recently been shown that targeted analysis of data independently acquired (DIA) peptide fragment ion spectra (SWATH-MS) has the potential to combine the scale of shotgun proteomics with the analytical accuracy of MRM [1]. We have developed the software Spectronaut for analysis of high content datasets which are typically produced in DIA mode. Spectronaut adapts algorithms of mProphet [2] providing fast and efficient processing of DIA data and accurate error statistics.