BoxCar Assisted MS Fragmentation (BAMF)

Abstract

A recent study described the utilization of complex quadrupole isolation schemes to reduce high abundance ion saturation in Orbitrap systems. The BoxCar technique effectively democratizes MS1 scans by restricting high abundance ions from consuming as much space in the trap. This restriction allows lower abundance ions more acquisition time and can increase the signal to noise by a full order of magnitude. While effective at the MS1 level, BoxCar does not show an improvement in MS/MS acquisition as ions selected for fragmentation must come from an additional MS1 full scan in the method. In this study we describe BoxCar Assisted MS Fragmentation (BAMF), wherein ions for fragmentation are selected directly from the BoxCar scans. When utilizing BAMF, we observe the identification of ions by MS/MS that are not at all detectable in the MS1 scans of identical concentrations of peptides analyzed by standard data dependent acquisition experiments.