Spatial Proteomics Using Mass Spectrometry

Course Description

Spatial proteomics methods are used for studying the organization and the function of proteins in their local micro-environment. Most imaging approaches can determine the spatial distribution of proteins at single-cell resolution, typically focusing on a small number of proteins but lacking the throughput necessary to achieve comprehensive proteome quantification.

The objective of this course is to introduce mass spectrometry (MS)-based spatial proteomics, employing liquid-chromatography (LC) or matrix-assisted laser desorption/ionization (MALDI) imaging MS methods.

The participants will learn how the field evolved from the analysis of entire tissues to the combination of laser-assisted microdissection and LC-MS proteomics for the simultaneous quantification of hundreds to thousands of proteins in specific regions of interest. Moreover, they will become aware of the potential of using MALDI-MS imaging approaches to integrate the spatial analysis of target proteins and other classes of biomolecules (i.e. glycans, small molecules).

The course is designed to bring theory and practice together and introduce the participants to basics MS-based spatial proteomics workflows, including sample preparation, state-of-the-art mass spectrometry, and software for data analysis.

Short Course Program:

1. Introduction to spatial proteomics
2. Basics of LC and MALDI-MS technologies and workflows:

• Analytical strategies
• Sample preparation
• High-resolution nanoLC-MS/MS
• MALDI-MS imaging

3. Experiment planning, data analysis and interpretation:

• Importance of experimental design
• Basics of protein identification and quantification
• Software solutions
• IT and awareness of the data storage and its size
• Spatial clustering
• Multimodal considerations  

Learning outcomes

By the end of this course, participants should be able to:

• Summarize the principles of current mass spectrometry-based spatial proteomics technologies and applications
• Understand basic spatial proteomics sample preparation methods for the characterization of protein expression in tissue slides, by using laser microdissection LC-MS workflows and MALDI-MS imaging.
• Perform basic data analysis and evaluate the MS results
• Know what to expect - understand the opportunities, differences and limits of spatial MS proteomics approaches  

Participants

The course is limited to 8 participants only.

Target audience and prerequisites

Doctoral students and post-doctoral scientists in Biology and Biomedicine, actively engaged in or soon to commence research involving spatial proteomics using mass spectrometry. It is not essential to have any previous knowledge of the subject area. A minimal previous knowledge and understanding of analytical chemistry is highly recommended.

Changes to the course dates

The FGCZ reserves the right to postpone the course to a later date should the number of applicants be lower than six. Further questions? Check out the FAQ for Courses  

Please note, that the above prices can only be applied if the tuition fee is paid through an internal, i.e. University of Zurich or ETHZ, account (valid Kostenstelle/PSP-Element).

An invoice will be issued upon registration. Registered participants will receive an email containing an “Application Form”, which must be signed by their respective supervisor.

The signed form should then be returned to the FGCZ via email as a PDF. Only upon receipt of the signed “Application Form”, will the participant’s registration be considered complete, and their place in the course officially confirmed.

Cancellation Policy

Please note that, due to the high demand for this course, any change  related to your participation must be communicated as soon as possible, but not later than twenty (20) working days prior to the course start date. The notice must be sent via email to . If the cancellation of the course occurs after this time period, the tuition fee will not be refunded.