Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge

Spectral pre-processing to remove precursor peaks and their associated neutral losses prior to protein sequence library searches resulted in a 9.8% increase in peptide identifications at a 1% False Discovery Rate [FDR] compared to previous OMSSA filter. Modifications to the OMSSA noise filter to accommodate various ion-types resulted in a further 4.2% increase in peptide identifications at 1% FDR. Moreover, ETD spectra when searched with charge states obtained from the precursor charge determination algorithm is shown to be up to 3.5 times faster than the general range search method, with a minor 3.8% increase in sensitivity.Overall, there is an 18.8% increase in peptide identifications at 1% FDR by incorporating the new precursor filter, noise filter and by using the charge determination algorithm, when compared to previous versions of OMSSA.Mass-spectrometry based proteomics is a major technique for the identification of the constituents of complex protein mixtures [1]. Analysis of peptide and protein sequences using gas-phase ion chemistry and tandem mass spectrometry has been described by various groups [2-5], where common methods of peptide identification involve enzymatic digestion of proteins isolated from protein mixture, fractionation and fragmentation of the resultant peptides, followed by MS/MS sequence search algorithms to match the peptide sequence to the tandem mass spectrometry data. Some of the widely used search algorithms are OMSSA [6], X!Tandem [7], Sequest [8], MyriMatch [9], SpectrumMill (Agilent) and Mascot [10]. A key step is the fragmentation method used to dissociate the peptides obtained after enzyme cleavage. Techniques currently used include Collision Activated Dissociation [CAD], Electron Capture Dissociation [ECD] and ETD [11]. The use of ETD is becoming increasingly prevalent as it can be used on more common instruments such as quadrupole ion trap.ETD/ECD spectra can contain precursor peaks in various charge states, called charge reduc