A Comprehensive Comparison of the de novo Sequencing Accuracies of PEAKS, BioAnalyst and PLGS

1. Introduction To identify proteins, a de novo sequencing algorithm computes the peptide sequences from MS/MS data without the need of a protein database. When proteins are heavily modified or from an organism whose genome is not sequenced, de novo sequencing is the only reliable approach to identify the proteins in a sample. De novo sequencing typically requires higher quality data than those required by a database search method. Therefore, a hybrid quadrupole time-of-flight (Q-TOF) instrument is most often used for measuring the MS/MS data. There are three commercial de novo sequencing software packages commonly used for the analysis of Q-TOF MS/MS data: BioAnalyst for the MDS Sciex/ABI QSTAR, PLGS for Micromass/Waters Q-TOFs, and PEAKS 1 for both. In this poster we compare the accuracies of the three packages.