Mass Spectrometry-Based Proteomics: Basic Principles and Emerging Technologies and Directions

Abstract

As the main catalytic and structural molecules within living systems, proteins are the most likely biomolecules to be affected by radiation exposure. Proteomics, the comprehensive characterization of proteins within complex biological samples, is therefore a research approach ideally suited to assess the effects of radiation exposure on cells and tissues. For comprehensive characterization of proteomes, an analytical platform capable of quantifying protein abundance, identifying post-translation modifications and revealing members of protein complexes on a system-wide level is necessary. Mass spectrometry (MS), coupled with technologies for sample fractionation and automated data analysis, provides such a versatile and powerful platform. In this chapter we offer a view on the current state of MS-proteomics, and focus on emerging technologies within three areas: (1) New instrumental methods; (2) New computational methods for peptide identification; and (3) Label-free quantification. These emerging technologies should be valuable for researchers seeking to better understand biological effects of radiation on living systems.

A proteomic approach to obesity and type 2 diabetes

“…The first group comprises methods that are based on the ion count and compare either maximum abundance or volume of ion count for peptide peaks at specific retention times between different samples. Since ionized peptides elute from a reversed‐phase column into the mass spectrometer, their ion intensities can be measured within the given detection limits of the experimental setup (Fig. shows in a simple manner the scheme of Label‐free useful for metabolic research).…”

Recent technological developments in proteomics shed new light on translational research on diabetic microangiopathy

“…MS1 and MS2 spectra for each sample are acquired and the individual peptide properties are compared between the individual measurements. Spectral counting and intensity‐based measurements are two major methods for label‐free MS‐based quantitative proteomics . Moreover, the method named the total protein approach was developed.…”

A mass spectrometric insight into the origins of benign gynecological disorders

“…During the early era of medicinal manufacturing, MS was instrumental in identifying metabolites of a lead compound, determining pharmacological action and toxicity (Mano & Goto, 2003). Recently, its application has expanded to analyze biological samples via omics investigations, particularly proteomics and metabolomics (Pujos-Guillot et al, 2013;van Riper et al, 2013). Proteomics is an analytical platform quantifying protein abundance, identifying post-translational modifications, and revealing protein complexes members on a systemic scale (van Riper et al, 2013).…”

“…Recently, its application has expanded to analyze biological samples via omics investigations, particularly proteomics and metabolomics (Pujos-Guillot et al, 2013;van Riper et al, 2013). Proteomics is an analytical platform quantifying protein abundance, identifying post-translational modifications, and revealing protein complexes members on a systemic scale (van Riper et al, 2013). Metabolomics has provided insight into cell metabolism and bioenergetics by identifying and quantifying small-molecule metabolites within an organism (D' Alessandro et al, 2012;Milne et al, 2013).…”