ACS Publications Symposium

Innovation in Measurement Science - Bruker Sponsored Session

This session took place on June 24, 2021

Symposium Overview

This session discusses the PASEF, dia-PASEF and prm-PASEF methods and explains how these methods allow researchers to perform proteomics faster, with better depth of coverage, better sensitivity, and with more confidence in their identification and quantitation.

After a summary of these methods, this session covers some of the latest applications of the timsTOF Pro and 4D-Proteomics technology to biomarker discovery and validation, immunopeptidomcs and single cell proteomics.


  • Features and performance of 4D-Proteomics on the timsTOF Pro
  • PASEF, dia-PASEF, prm-PASEF
  • High throughput biomarker discovery and validation
  • Ultra-high sensitivity for immunopeptidomics and single cell proteomics

Latest Applications of 4D-Proteomics using the timsTOF Pro and recent developments in ultra-high sensitivity and single cell proteomics

Gary Kruppa, Ph.D., Vice President Proteomics at Bruker Daltonics Inc., and Managing Director of Bruker S.R.O., Billerica, MA, USA

Gary Kruppa serves as the Vice President for Proteomics at Bruker Daltonics Inc. He manages a growing global team of applications, field applications and applications development scientists, focused on developing new proteomics applications for the timsTOF Pro, and supporting customers and collaborators.  Dr. Kruppa earned his bachelor’s degree in chemistry at the University of Delaware and his Ph. D. in chemical physics at CalTech. Dr. Kruppa has been working with Bruker since 1991, where he first worked on the FTMS product line, later serving as Vice President for FTMS. From 2001 to 2004, Dr. Kruppa ran his own research lab at Sandia National Labs, where he and his team developed novel methods and reagents for chemical crosslinking of proteins for the study of protein structure. In 2004 he rejoined Bruker, where he served as Vice President for Business Development until 2014. From 2014 to 2016 Dr. Kruppa worked as CEO of MRM Proteomics Inc., to commercialize kits for quantitative MRM proteomics analysis of potential biomarkers. Dr. Kruppa returned to Bruker in 2016 to serve as Vice President for proteomics, where he helped launch the revolutionary timsTOF Pro QTOF Mass Spectrometer powered by the PASEF method.

4D-Proteomics – Dissecting the 3D Structure of Proteins Through Ion Mobility Enhanced Crosslinking Mass Spectrometry

Richard Scheltema, Ph.D., Assistant Professor, Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands

Richard currently runs his own, independent research group at Utrecht University. After finalizing his PostDoc working on LC-MS/MS platforms within the group of Prof. Dr. Matthias Mann (Max Planck Institute of Biochemistry, DE), he started the Scheltema laboratory at Utrecht University. The focus lies on structural proteomics applied to medium and high complexity protein environments like the ECM and membrane proteins. Mass spectrometry based approaches are employed that are independent of protein size, deal with high complexity mixtures and play well with other structural biology techniques like Cryo-EM and crystallography to uncover novel and exciting biology. The technological developments and their applications have been published in journals like Nature Protocols, Nature Communications, Molecular Cell, Cell Reports, ACS Central Science, and PNAS and additionally have been commercialized and are worldwide in use.


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