Comparison of Acquisition Methods for Linear Quadrupole Ion Trap-Fourier Transform Cyclotron Resonance Mass Spectrometer in Shotgun Proteomics

Mass spectrometers with high accuracy and high resolution,such as FT-ICR have been widely used in proteomic studies in recent years.To compare the effectiveness of various data acquisition methods in shotgun proteomics,we used a linear quadrupole ion trap-Fourier transform ion cyclotron resonance(LTQ-FT) mass spectrometer to analyze two peptide mixtures with different complexity by different acquisition strategies.For the peptide mixture of four standard proteins,sequence coverage obtained by selected ion monitoring scans(SIM3) was 1.51 to 1.9 fold than that by survey MS scans(FT10).For the peptide mixture of yeast proteins,the strategy of only acquiring double and triple charged ions(FT_23) got 64.1% more MS/MS spectra identifications than that of total acquisition of single,double and triple charge ions(FT_123).Finally,the features of the spectrum obtained with different acquisition mode were also compared.In conclusion,optimal acquisition methods are needed for the samples with different complexity.