Highly Multiplexed Targeted Proteomics Acquisition on a TIMS-QTOF / Leveraging prm-PASEF® on the timsTOF Pro to Interrogate the Functional Proteome

This webinar took place on April 28, 2021

Webinar Overview - Part I: Highly Multiplexed Targeted Proteomics Acquisition on a TIMS-QTOF

The new tims-TOF pro-mass spectrometer offers improved capabilities for the targeted acquisition. The prm-PASEF® method uses the multiplexing capability provided by the trapped ion mobility separation, allowing more than 200 peptides to be monitored over a 30 min liquid chromatography separation. Compared to conventional parallel reaction monitoring (PRM), precursor ions are accumulated in the TIMS cells and separated according to their shape and charge before eluting into the Q-TOF part of the mass spectrometer. Using these improved mass spectrometric capabilities, we detected and quantified 216 isotope-labeled synthetic peptides (AQUA peptides) spiked in HeLa human cell extract with limits of quantification of 17.2 amol for some peptides. The method's applicability is demonstrated by measuring Kras, Nras, and Hras in biological samples and the most common cancer-associated Kras mutations.

Webinar Overview - Part II: Leveraging prm-PASEF® on the timsTOF Pro to Interrogate the Functional Proteome

Integrated TIMS with PASEF® affords an opportunity for highly selective, rapid detection and reproducible quantification of peptides in complex matrices. Here we describe PASEF-PRM-LIVE, a framework implementing on-the-fly adjustment of the detection window to maximize target coverage. This platform is ideally suited for functional protein profiling.

  • PRM-LIVE accounts for potential retention time drift of peptides across multiple LC analyses
  • PRM-LIVE provides for reproducible quantification of nearly 2,000 peptides in complex cellular proteomes
  • PRM-LIVE provides a powerful platform for profiling the binding behavior of selective small molecule inhibitors

Speaker Part I

Prof. Dr. Gunnar Dittmar
Group leader proteomics of cellular signalling
Luxembourg Institute of Health, Department of Infection and Immunity

Prof. Dr. Gunnar Dittmar is the Head of proteomics of cellular signalling group at the LIH’s Quantitative Biology Unit. He has a strong background in proteomics, bioinformatics, chemistry and biochemistry. He completed a PhD in cell biology at the DKFZ (German Cancer Research Centre), in Heidelberg in 1997, followed by six years at the Harvard Medical School in Boston (USA), first as a postdoctoral fellow and later as an instructor of Cell Biology.

Back to Germany, he was recruited as a group leader at the Max Delbrück Center for Molecular Medicine (MDC), in Berlin in 2003. In 2007, he established the Mass Spectrometry Core Unit at MDC, and in 2014 he additionally built up the Proteomics Unit of the Berlin Institute of Health (BIH), a translational research centre resulting from the joint forces of MDC and the Charite´ – medical school of the Freie and Humboldt University, Berlin. During these years, he further intensified his knowledge in proteomics and mass spectrometry techniques, oriented towards a clinical perspective.

Since 2011 he is a visiting professor at the Technion University in Haifa, Israel. In 2016 he was recruited to the Luxembourg institute of health (LIH) where he created the new proteomics research group, a bioinformatics group and built the new multi-centre LuxGen NGS sequencing platform (a joined effort of the LIH and LNS – Laboratoire National de Sante´). Starting in 2018 he worked on setting up the new quantitative biology unit, which was officially inaugurated in 2019. The unit consists of ten different technology-oriented groups and platforms, spanning from bioinformatics to in vivo imaging. Since 2019 he has been appointed as an affiliated professor for proteomics at the University of Luxembourg.

Speaker Part II

Jarrod A. Marto, Ph.D.
Associate Professor, Dept. of Pathology
Brigham and Women’s Hospital and Harvard Medical School, Dana-Farber Cancer Institute

Dr. Marto received his Ph.D. in analytical chemistry at The Ohio State University with Alan Marshall and went on to postdoctoral studies at the University of Virginia with Don Hunt.

After several years in the biotech sector, Dr. Marto joined the Dana-Farber Cancer Institute in 2004. Dr. Marto uses mass spectrometry as a primary discovery tool to understand how genomic alterations, environmental insults, or the action of small molecule chemical probes impact the functional proteome, including protein post-translational modifications, biochemical complexes, signaling pathways, or how they manifest en masse as phenotypic or disease signatures.

Dr. Marto’s research is further enabled by development of advanced chromatographic separation platforms which provide improved peptide detection and quantification, and support genome-scale interrogation of mammalian proteomes. In addition, his lab builds open-source computation tools that facilitate interrogation of mass spectrometry data across the full spectrum of scientific inquiry, from the underlying instrumentation to interpretation of quantitative proteomic data in the context of biological pathways. His research program represents a productive convergence of biology, computation, and analytical science.


For Research Use Only. Not for use in clinical diagnostic procedures.