Advances in targeted proteomics and applications to biomedical research

Abstract

Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.

Quantitative Proteomic Analysis of Human Airway Cilia Identifies Previously Uncharacterized Proteins of High Abundance

“…More recently, a number of approaches have been employed enabling the quantification of absolute molar amounts of one or more proteins within a sample. For example, multiple reaction monitoring (MRM) utilizing triple-quadrupole MS systems, an approach utilized extensively in small molecule quantification in complex sample matrices, has been applied in conjunction with isotopically labeled peptide standards to quantify selected target proteins of interest in complex biological samples (40). Unfortunately, this hypothesis-driven approach requires that one knows beforehand which protein(s) are of interest and has in hand synthetic peptide standards corresponding to these targeted proteins (41).…”

Unbiased and targeted mass spectrometry for the HDL proteome

“…The approach is very sensitive, accurate and convenient if antibodies are not available; and is often used in validation experiments following global proteomics studies [2]. Multiple reaction monitoring (MRM), or sometimes referred to as selected reaction monitoring (SRM), is the most used targeted MS method [20]. MRM is best performed on a quadrupole instrument that is specialized for isolating, one at a time, a predefined list of peptides for subsequent fragmentation, followed by isolation of a single fragment ion (transition) for detection (Fig.…”

“…An alternative to MRM that has emerged in recent years is PRM, parallel reaction monitoring. Unlike MRM that is performed on a triple quadrupole instrument that scans at unit resolution (~1Da), PRM is performed on the high resolution/accurate mass (HR/AM) quadrupole Orbitrap instrument (HR-MRM for the quadrupole time-of-flight instrument) that scans up to a resolution of 240 K (at 200 m/z ) [20–22]. A major advantage of PRM over MRM is that it is permissible to larger isolation windows since its HR/AM scans can differentiate target ions from background ions (Fig.…”

Mass spectrometry-based proteomic exploration of the human immune system: focus on the inflammasome, global protein secretion, and T cells

“…Several studies have used this approach to characterize changes in sub-cellular proteomes due to viral infection [5,6] and other stimuli activating innate immune responses [7,8]. In addition to global screening, MS-based proteomics provides methods for targeted protein quantification (reviewed in [9]). …”