Topic outline

  • General

    Introduction to Mass-Spectrometry based Proteomics

    Lausanne, 15 April 2011

    The goal of this course is to give some basic theoretical and practical knowledge on the mass spectrometry (MS) techniques used in proteomics to identify proteins in simple and complex mixtures. The course will cover the following main subjects:
    • Fundamental concepts of mass spectrometry (MS) of peptides and proteins
    • Strategies for protein identification with MS data: theory, concepts, variants
    • Database searches with MS data: practical examples and exercises
    • Validation and interpretation of results
    • Workflows and examples of applications.

    The course will be structured with alternating theory and exercise periods. All participants will learn how to analyze simple mass spectrometry data and how to use an online tool for protein identification. They will also be introduced to a data processing software (Scaffold) used to filter, validate, compare and export complex proteomics results. Examples of typical proteomics workflows will be presented.


    Manfredo Quadroni (UNIL, PAFL)
    Patrice Waridel (UNIL, PAFL)


    Participants should bring a pocket calculator. A laptop with wireless connectivity is mandatory.
    The software Scaffold 3 must be installed and can be downloaded from
    (Note: no key is required to use Scaffold as a viewer).

    Practical organization - Location

    Sessions runs from 9:00 to 17:00 approximately, with a lunch break.
    This one-day course is held at the Génopode building (Auditorium B) of the University of Lausanne.


    The course is currently full and the registration is closed.
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