Advances in high-resolution accurate mass spectrometry application to targeted proteomics

Targeted quantitative proteomic analyses aim at systematically measuring the abundance of proteins in large sets of samples, without biases or missing values. One typical implementation is the verification of biomarker candidates in bodily fluids, which measures extended lists of validated transitions using triple quadrupole instruments in selected reaction monitoring (SRM) mode. However, the selectivity of this mass spectrometer is limited by the resolving power of its mass analyzers, and interferences may require the reanalysis of the samples. Despite the efforts undertaken in the development of software, and resources to design SRM studies, and to analyze and validate the data, the process remains tedious and time consuming. The development of fast scanning high-resolution and accurate mass (HRAM) spectrometers, such as the quadrupole TOF and the quadrupole orbitrap instruments, offers alternatives for targeted analyses. The selectivity of HRAM measurements in complex samples is greatly improved by effectively separating co-eluting interferences. The fragment ion chromatograms are extracted from the high-resolution MS/MS data using a narrow mass tolerance. The entire process is straightforward as the selection of fragment ions is performed postacquisition. This account describes the different HRAM techniques and discusses their advantages and limitations in the context of targeted proteomic analyses.