title: A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition.
abstract: Mass spectrometry (MS) based proteomics have achieved a near-complete proteome coverage in humans and in several other organisms, producing a wealth of information stored in databases and bioinformatics resources. Recent implementation of selected/multiple reaction monitoring (SRM/MRM) technology in targeted proteomics introduced the possibility of quantitatively follow-up specific protein targets in a hypothesis-driven experiment. In contrast to immunoaffinity-based workflows typically used in biological and clinical research for protein quantification, SRM/MRM is characterized by high selectivity, large capacity for multiplexing (approx. 200 proteins per analysis) and rapid, cost-effective transition from assay development to deployment. The concept of SRM/MRM utilizes triple quadrupole (QqQ) mass analyzer to provide inherent reproducibility, unparalleled sensitivity and selectivity to efficiently differentiate isoforms, post-translational modifications and mutated forms of proteins. SRM-like targeted acquisitions such as parallel reaction monitoring (PRM) are pioneered on high resolution/accurate mass (HR/AM) platforms based on the quadrupole-orbitrap (Q-orbitrap) mass spectrometer. The expansion of HR/AM also caused development in data independent acquisition (DIA). This review presents a step-by-step tutorial on development of SRM/MRM protein assay intended for researchers without prior experience in proteomics. We discus practical aspects of SRM-based quantitative proteomics workflow, summarize milestones in basic biological and medical research as well as recent trends and emerging techniques.
authors.affiliation: Masaryk University, Research Centre for Toxic Compounds in the Environment, Kamenice 753/5, 625 00, Brno, Czechia.
authors.forename: Veronika
authors.initials: V
authors.lastname: Vidova
authors.affiliation: Masaryk University, Research Centre for Toxic Compounds in the Environment, Kamenice 753/5, 625 00, Brno, Czechia. Electronic address: spacil@u.washington.edu.
authors.forename: Zdenek
authors.initials: Z
authors.lastname: Spacil
mesh_terms: D006801:Humans; D013058:Mass Spectrometry; D011499:Protein Processing, Post-Translational; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D020543:Proteome
keywords: Data independent acquisition (DIA); Parallel reaction monitoring (PRM); Selected/multiple reaction monitoring (SRM/MRM); Sequential windowed acquisition of all theoretical fragmentation spectra (SWATH); Tandem mass spectrometry (MS/MS); Targeted quantitative proteomics tutorial