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Transfer of Optimized Acquisition Parameters Between Mass Analyzer Types for Improved Protein Identification and Quantification

Abstract: Putative protein biomarker candidates must be validated by performing targeted quantitative analyses with patient samples. The most common MS/MS approach has been to generate a highly specific and sensitive MRM-based assay for peptides seen in the discovery process. However, optimization of the selected peptides can be a time-consuming process. The traditional discovery approach has used ion trap based methodology, which can produce substantially different fragment patterns than triple quadrupole mass spectrometers. Using shared collision cell design, Q1 selection ability, nanoflow LC/MS interface and nanoflow-based chromatography, this work examines using information from a biomarker discovery experiment run on a Q-TOF to speed validation assay development for a MRM-based workflow on a triple quadrupole system.

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