title: Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective.
abstract: Quantitative mass spectrometry is a rapidly evolving methodology applied in a large number of omics-type research projects. During the past years, new designs of mass spectrometers have been developed and launched as commercial systems while in parallel new data acquisition schemes and data analysis paradigms have been introduced. Core facilities provide access to such technologies, but also actively support the researchers in finding and applying the best-suited analytical approach. In order to implement a solid fundament for this decision making process, core facilities need to constantly compare and benchmark the various approaches. In this article we compare the quantitative accuracy and precision of current state of the art targeted proteomics approaches single reaction monitoring (SRM), parallel reaction monitoring (PRM) and data independent acquisition (DIA) across multiple liquid chromatography mass spectrometry (LC-MS) platforms, using a readily available commercial standard sample. All workflows are able to reproducibly generate accurate quantitative data. However, SRM and PRM workflows show higher accuracy and precision compared to DIA approaches, especially when analyzing low concentrated analytes.
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr, Zurich, Switzerland.
authors.forename: Tobias
authors.initials: T
authors.lastname: Kockmann
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr, Zurich, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: Trachsel
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr, Zurich, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: Panse
authors.affiliation: AstraZeneca Nucleotide Bioanalysis, Drug Safety and Metabolism, Innovative Medicines Mölndal, Sweden.
authors.forename: Asa
authors.initials: A
authors.lastname: Wahlander
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr, Zurich, Switzerland.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Selevsek
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr, Zurich, Switzerland.
authors.forename: Jonas
authors.initials: J
authors.lastname: Grossmann
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr, Zurich, Switzerland.
authors.forename: Witold E
authors.initials: WE
authors.lastname: Wolski
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr, Zurich, Switzerland.
authors.forename: Ralph
authors.initials: R
authors.lastname: Schlapbach
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics / Q000379:methods*
keywords: LC-MS; Label-free; Targeted proteomics; Technology