A Tandem Mass Spectrometry Acquisition Strategy Based on Exclusion of Precursor Ions

Abstract

Because of the complexity of proteome samples, comprehensive analysis to characterize all proteins is still not possible with present methodologies. It has been shown that replicate runs could increase the number of identified proteins. However, the redundancy of protein identifications was high. High-abundance peptides tended to be repeatedly analyzed in different runs. To reduce the redundancy and improve the efficiency of identification, the tandem mass spectrometry (MS/MS) acquisition method of linear ion trap-Fourier transform ion cyclotron resonance mass spectrometry was studied, and an acquisition strategy based on exclusion of precursor ions was developed. It proved that the strategy could extremely reduce the redundancy of MS/MS acquisition and improve the efficiency of protein identifications.