Comparison and Evaluation of Different Acquisition Parameters in LTQ-FT and LTQ-Orbitrap Mass Spectrometers to Improve Protein Identification Rates

摘要

The number of MS/MS events in the LTQ-FT influences protein identification rates, but not in a consistent manner. In the LTQ-Orbitrap, generally, an increase in identification rates was observed with increasing the number of data dependent scans. Lawer ion injection times for MS/MS seems to increase peptide and protein identification rates in both the LTQ-FT and LTQ-Orbitrap mass analyzers. Increasing the number of ions for MS/MS experiments in the LTQ-FT results in a higher number of identified peptides, unique peptides and identified proteins, whereas in the LTQ-Orbitrap similar identification rates were obtained above a certain AGC target value.