High Resolution / Accurate Mass Targeted Proteomics

Targeted proteomics has emerged as the predominant method for quantitative analyses of peptides to complement shotgun LC/MS studies. Targeted measurements are routinely performed using the technique of selected reaction monitoring (SRM) on triple quadrupole instruments. However, the approach suffers from limitations inherent to the SRM technique. First, the selectivity of measurements is often insufficient to effectively discriminate the analytes from the complex background commonly encountered in biological samples. Second, the number of peptides analyzed in one experiment remains limited. The recent development of high resolution/accurate mass instruments, in conjunction with various acquisition methods, has opened new avenues for quantitative proteomic studies. An overview of the analytical capabilities of a high resolution hybrid quadrupole–orbitrap instrument for quantitative applications is presented and discussed in this chapter. The measurements are performed either on precursor ions (selected ion monitoring mode) or on fragment ions (parallel reaction monitoring mode), which overcome, in many instances, the selectivity issue encountered in complex samples, as illustrated on various examples. It clearly demonstrates the potential of high resolution mass measurements for quantitative proteomic applications.