title: Strategies in relative and absolute quantitative mass spectrometry based proteomics.
abstract: Quantitative mass spectrometry approaches are used for absolute and relative quantification in global proteome studies. To date, relative and absolute quantification techniques are available that differ in quantification accuracy, proteome coverage, complexity and robustness. This review focuses on most common relative or absolute quantification strategies exemplified by three experimental studies. A label-free relative quantification approach was performed for the investigation of the membrane proteome of sensory cilia to the depth of olfactory receptors in Mus musculus. A SILAC-based relative quantification approach was successfully applied for the identification of core components and transient interactors of the peroxisomal importomer in Saccharomyces cerevisiae. Furthermore, AQUA using stable isotopes was exemplified to unraveling the prenylome influenced by novel prenyltransferase inhibitors. Characteristic enrichment and fragmentation strategies for a robust quantification of the prenylome are also summarized.
authors.affiliation: Ruhr-University Bochum, Medizinisches Proteom-Center, Universitätsstraße 150, D-44801 Bochum.
authors.forename: Claudia
authors.initials: C
authors.lastname: Lindemann
authors.affiliation: Ruhr-University Bochum, Medizinisches Proteom-Center, Universitätsstraße 150, D-44801 Bochum.
authors.forename: Nikolas
authors.initials: N
authors.lastname: Thomanek
authors.affiliation: Ruhr-University Bochum, Biomolecular Mass Spectrometry, Universitätsstraße 150, D-44801 Bochum.
authors.forename: Franziska
authors.initials: F
authors.lastname: Hundt
authors.affiliation: Ruhr-University Bochum, Medizinisches Proteom-Center, Universitätsstraße 150, D-44801 Bochum.
authors.forename: Thilo
authors.initials: T
authors.lastname: Lerari
authors.affiliation: Ruhr-University Bochum, Medizinisches Proteom-Center, Universitätsstraße 150, D-44801 Bochum.
authors.forename: Helmut E
authors.initials: HE
authors.lastname: Meyer
authors.affiliation: Ruhr-University Bochum, Biomolecular Mass Spectrometry, Universitätsstraße 150, D-44801 Bochum.
authors.forename: Dirk
authors.initials: D
authors.lastname: Wolters
authors.affiliation: Ruhr-University Bochum, Medizinisches Proteom-Center, Universitätsstraße 150, D-44801 Bochum.
authors.forename: Katrin
authors.initials: K
authors.lastname: Marcus
mesh_terms: D000818:Animals; D002462:Cell Membrane / Q000378:metabolism; D002923:Cilia / Q000378:metabolism; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000378:metabolism
keywords: AQUA; LC-MS/MS; SILAC; label-free; prenylation; protein-protein interactions