Proteomic DACH User Group Meeting 2025

Welcome & Introduction

Dr. Quentin Enjalbert, Head of EU Sales, PreOmics

Maximizing Efficiency and Quality: How APP96^TM is enhancing productivity and throughput by saving time in preparing high quality samples for total proteome quantifications, interaction proteomics and protein quality checkups

Barbara Steigenberger, Head of Mass Spectrometry Core Facility at Max Planck Institute of Biochemistry, Mass Spectrometry Core Facility, Munich, Germany

Optimization of Sample Processing Workflows for Comprehensive Proteome Profiling in Large Clinical Studies.

Dr. Karim Aljakouch, Postdoctoral Researcher, Division of Proteomics of Stem Cells and Cancer, DKFZ German Cancer Research Center, Heidelberg, Germany.

Improve biomarker discovery with ENRICH technology: An enrichment-based workflow for plasma allows rapid, in-depth analysis of clinical cohorts

Klaus Kratochwill, Leiter Core Facility Proteomics, Translational Biomedical Researcher, Biochemist and Omics Specialist, Medizinische Universität Wien, Austria

Q&A session

Open questions to the speakers and PreOmics team (in German/English language)

In proteomics research, efficient and reproducible sample preparation is essential for high-throughput analyses and reliable results. In this presentation, I will demonstrate how the APP96™ sample preparation robot enhances productivity by streamlining workflows and reducing preparation time. By automating complex sample handling processes, the APP96™ ensures consistent, high-quality outcomes across a range of proteomics applications, including total proteome quantification, interaction proteomics, and protein quality assessments. Hands-on time is reduced.

Drawing from practical experience in my proteomics facility, I will present key examples where APP96™ has performed exceptionally well in sample preparation. These include protein quality control, total proteome quantification, and LiP-MS (Limited Proteolysis Mass Spectrometry) studies, highlighting the robot's versatility for different sample types.

As a part of SMART-CARE, we have established a robust and standardized MS-based proteomics pipeline from sample collection, sample processing to LC-MS data acquisition and data analysis to analyze large clinical sample cohorts. To achieve this: i) We have implemented an automated single-pot solid-phase-enhanced sample preparation workflow (autoSP3) on a liquid handling robot for automated processing of various sample types including tissues and body fluids. ii) We developed a single-sample workflow for integrative metabolome and proteome analysis (MTBE-SP3). iii) We further optimized the sample processing workflow for formalin-fixed, paraffin-embedded (FFPE) tissues using BeatBox, ensuring improved protein recovery and compatibility with downstream MS-based proteomics.

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Proteomics DACH User Group Meeting

OVERVIEW

Proteomics DACH User Group Meeting

AGENDA

SPEAKERS & ABSTRACTS

Barbara Steigenberger, Head of Mass Spectrometry Core Facility at Max Planck Institute of Biochemistry, Mass Spectrometry Core Facility, Munich, Germany

Dr. Karim Aljakouch, Postdoctoral Researcher, Division of Proteomics of Stem Cells and Cancer, DKFZ German Cancer Research Center, Heidelberg, Germany.

Klaus Kratochwill, Leiter Core Facility Proteomics, Translational Biomedical Researcher, Biochemist and Omics Specialist, Medizinische Universität Wien, Austria

Dr. Quentin Enjalbert, Head of EU Sales, PreOmics