Short-Course Program MSB'2006

Sunday. 22. January

Morning, 10.00 – 12.30 hrs Afternoon, 13.30 - 16.00 hrs
The short-courses are aimed at learning fundamentals and applications of an important MicroScale separation technology. A short-course will encompass the theoretical basis, the scope and modes of the separation technology, application in analysis in the life sciences and chemical analysis and practical hints for day to day practice. Short courses will last a full day. 
  • Coupling MicroScale Bioanalysis with Mass Spectrometry for Protein and Peptide Analysis 

Rainer Bischoff1 and Hjlamar Permentier2, 1Department of Analytical Biochemistry and 2Mass Spectrometry Core Facility, Center of Pharmacy, University of Groningen, The Netherlands 

Sample preparation and separation on a micro-scale are critical for the analysis of low-abundance proteins and peptides in complex biological matrices. This short-course will give an introduction to sample handling and preparation of bio-fluids (e.g. serum, urine), tissue (e.g. obtained by laser capture micro-dissection) or cell culture material. Emphasis will be placed on analytical systems, where sample preparation is an integral step in the overall procedure. Furthermore, proteolytic digestion using on-line enzymatic reactors will be highlighted.

Following sample preparation, the analytes of interest need to be separated in miniaturized systems. In this short-course, we will focus on nano-HPLC and chip-based approaches coupled on-line (electro-spray ionization) or off-line (MALDI) to mass spectrometry. The various ionization methods and interfaces will be discussed as well as the range of mass analyzers with their advantages and disadvantages. The topic of quantitative proteomics based on stable-isotope labeling will be discussed.

The short-course will highlight applications from the author’s lab but also important work published in the literature. Going over these applications will have the purpose of showing how the individual “unit operations” can be combined and integrated in analytical systems capable of analyzing complex proteomics samples. Another part will focus on data processing and analysis, which is a critical part in comparative bio-analytical studies with LC-MS.

The objective of this course will be to instruct active proteomics researchers in the use of a suite of software tools designed for the analysis, validation, storage and interpretation of data obtained from large-scale quantitative proteomics experiments using stable isotope labeling method, multi-dimensional chromatography and tandem mass spectrometry. At the end of the course each participant will receive a CD containing additional reading material, the latest release of the proteomics tools presented as well as sample proteomics data and copies of other software tools developed at the ISB for systems biology data analysis and integration, specifically, Cytoscape and SBEAMS. The course will include:

  1. lectures describing a high-level view of the flow of information through the pipeline and algorithms used at each level of the analysis process
  2. demonstration of the software applied to real proteomics data
  3. information on where to find searchable help archives, get support, report problems, and suggest new features
  4. demonstration of installation of the software on laptops that have the necessary prerequisite software
    ( Windows: Required – Windows NT, 2000, or XP with Internet Information Server  installed, disk formatted with NTFS filesystem. Desirable – Bioworks Xcalibur)