Proteomics > Proteomics User Lab

FGCZ Proteomics User Lab

User Lab Guidelines

FGCZ User Guidelines


The Proteomics User Lab is offered to UZH/ETH users, who
  • plan to perform long term proteomics experiment (at least over 1 year, running multiple experiments)
  • design mass spectrometry-intense projects (e.g., with 100s of samples)
  • are interested in non-standard protocols that we do not offer in service mode
  • are motivated to develop new protocols

User Lab Course - Operator license

As of January 2022, we improved the structure of our trainings and all new users are requested to complete a short User Lab Course prior to starting a new project.
The course includes both self-paced and on-site learning modules, covering a theoretical and a practical introduction to mass spectrometry-based proteomics. At the end of the course, each user will receive an "Operator License" certificate, who will give access to our LC-MS instruments, analytical equipment, and software infrastructure.

How to enroll

If you do not have any running FGZC project, contact us at proteomics at fgcz.ethz.ch. You will be asked to submit a project in our B-Fabric data management system
Alternatively, please contact the coach of your FGCZ project!


The course consists of the following modules:

Module number TitleTopics TypeEstimated durationNotes
M1Project management using B-Fabric Basic concepts of an user lab project at FGCZ;
Functionalities of our data management system
self-paced learning + self-assessment~2h
M2Introduction to proteomics and the basics of sample preparation Typical proteomics workflows;
Basics of mass spectrometry
self-paced learning + self-assessment, accessible only once M1 is completed)~2h
M3LC-MS Operations Start an LC-MS system and check the performances;
Access other instruments (i.e., HPLC, KingFisher)
in person, instructor led -accessible only once M1/M2 are completed1 day 2-3 persons
M4Data analysisAccessing the software infrastructure at FGCZ;
Basics of protein identification and quantification
self-paced learning + self-assessment, accessible only once M3 is completed)3-5h
M5Data analysis Q&A Dedicated time to discuss open data analysis questions in person, instructor led -accessible only once M4 is completed ~2-3h
M6Final testTest consisting of practical assignments and free text answersself-paced 1-3h (plus computational time)


The course is offered as follow:
  • Once a month (independently of the number of requesters)
  • or, as soon as 2 new users want to start a new project.

Created by paolo. Last Modification: 2023-10-28 20:48 by paolo.