The effect of interfering ions on search algorithm performance for electron-transfer dissociation data

Collision-activated dissociation and electron-transfer dissociation (ETD) each produce spectra containing unique features. Though several database search algorithms (e.g. SEQUEST, MASCOT, and Open Mass Spectrometry Search Algorithm) have been modified to search ETD data, this consists chiefly of the ability to search for c- and z(center dot)-ions; additional ETD-specific features are often unaccounted for and may hinder identification. Removal of these features via spectral processing increased total search sensitivity by similar to 20% for both human and yeast data sets; unique peptide identifications increased by similar to 17% for the yeast data sets and similar to 16% for the human data set.