Topic outline

  • General

    Protein Identification by Mass Spectrometry

    May 7, 2010

    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

    The course will be structured with alternating theory and exercise periods. All participants will learn how to analyse 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 1: no key is required to use Scaffold as a viewer)
    (Note 2: with Windows Vista and Windows 7, "User Account Control" should be turned off for using Scaffold).

    Practical organization - Location
    Sessions runs from 9:00 to 17:00 approximately, with a lunch break.
    This one-day course is held in the reading room 2019 at the Genopode Building (Quartier Sorge, 1015 Lausanne)

    Registration is closed.