Mass Spectrometry-based Proteomics I: Protein Identification

Date 2 February 2018
Speaker(s) Manfredo Quadroni, Patrice Waridel, Roman Mylonas
Fees 50 CHF
Cancellation deadline 26 Jan 2018
Application Closed
City Lausanne


This course is the first part of a 2-day course package. The second part, Mass-Spectrometry based Proteomics II: Quantification and Post-Translational Modifications, is more advanced and takes place one week later. Both courses are independent and subject to separate registration

The goal of this course is to present 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 is the first part of a 2-day (independent) course on proteomics, and it will cover the following 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.


This course is addressed to all students/scientists interested in the subjects of proteomics and mass spectrometry. Students are expected to have biochemistry knowledge of proteins to attend this course.

Learning objectives

The participants will be introduced to:

  • proteomics and mass spectrometry
  • typical proteomics workflows.

At the end of the course, the participants are expected to:

  • analyze simple mass spectrometry data
  • use an online tool for protein identification (Mascot)
  • validate and compare proteomics search results with Scaffold.


Knowledge / competencies

Knowledge of biochemistry (proteins) and basic computer skills (program install, but no programming) are required.


You are required to bring your own laptop and to install Scaffold software (more information later).


The registration fees for academics are 50 CHF. This includes course content material and coffee breaks. Participants from non-academic institutions should contact us before application.

Deadline for registration and free-of-charge cancellation is set is set to 24/01/2018. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

Venue and time

University of Lausanne, Génopode building, classroom 2020 (Metro M1 line, Sorge station).

The course will start at 9:00 and end around 17:00. Precise information will be provided to the participants on due time.

Additional information

Coordination: SIB Training Group

We will recommend 0.25 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact