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Detection of Fm-Pip (= 301 nm)UV detectionof the ivDde protecting groupat 301 nmComplete deprotectionFig. 2. Monitoring trace of the synthesis ofV*FYQEK*.For this purpose we established aquantification approach based onthe absolute quantification of theRNA polymerase multi-proteincomplex partners using anadapted stable isotope dilution(SID) mass spectrometry method.Internal standard peptidescarrying an mTRAQ ® reagentlabel were specifically synthesized.Quantification was performedusing a LC-MRM approachbased on differentially mTRAQ ®reagent labelled peptides.The developed method wasimproved by synthesis of a set ofmTRAQ ® reagent labeledpeptides. A set of 18 peptideswere identified by MS and usedfor biomarker quantification.Peptides of RNA polymerasemulti-protein complex ofBacillus subtilis were usedsuccessfully for absolute quantitationin LCMS experiments. Theknown stoichiometry of the coreenzyme RpoA:RpoB:RpoC 2:1:1could be shown.This method allows tosynthesize specific mTRAQ ® oriTRAQ ® reagent labelled peptidesfor the quantitation ofbiomarkers with LCMS. This fitsright into the strategy of discovery, verification and validation of candidate biomarkersusing mTRAQ ® or iTRAQ ® reagent chemistry.AcknowledgmentsJan Muntel, Sandra Maaß, Michael Hecker, Dörte Becher from the Institute for Microbiology,University Greifswald, Germany. This work was supported by the European Union (BaSysBio LSHG-CT-2006-037469).References1. Chhabra, S.R., et al. Tetrahedron Letters 39, 1603-1606 (1998).2. Rohwedder, B., et al. Tetrahedron Letters 39, 1175-1178 (1998).3. Wittmann, V., Seeberger, S. Angew. Chem. Int. Ed. Engl. 39, 4348-4352 (2000).4. Allison, L.A., et al. Cell 42, 599-610. (1985).151