The objective of the course is to present current trends for large-scale protein analysis. The course will provide an overview of typical proteomics applications used today, including principles, needs and challenges. The content covers both experimental methods as well as data analysis strategies with a focus on biomarker discovery and precision medicine.

The aim of the course is to provide the students with an introduction to current methods, challenges, and applications in the field of proteomics.  

After completion of the course, the student should be able to describe and discuss the possibilities, advantages, complexity, and drawbacks of various proteomics technologies. The student is also expected to be able to compare traditional methods with emerging technologies, suggest suitable approaches for specified applications, motivate their choice, speculate and argue about the future of proteomics technologies, participate in scientific discussions regarding proteomics technologies and critically evaluate scientific results. 

Lectures
The lectures are given by experts in their respective fields and cover the background of the proteomic topic, methods for mass spectrometry and affinity-based analyses and their applications in clinical or biological research. The course also includes insights into how proteomics data can be used to map large-scale protein expression and current bioinformatic strategies. The lectures span the majority of the course period and a few lectures require student preparations.

Lab work
The lab element will be performed in groups of 4-6 students each and the work done in research labs at Albanova and SciLifeLab where the students will practice the methods discussed. All lab sessions including the first information and last presentation sessions are mandatory and a lab report will be handed in per group.

Workshops
At the end of the course there are two interactive and mandatory workshops. Four PhD students and researchers are invited to talk about their ongoing projects and their presentations are followed by discussions both in smaller groups and in whole class.

Mandatory assignments
There are two additional mandatory assignments during the course. One is based on recorded online lectures and one is the preparation for a flipped classroom lecture.

• Recommended articles and slides from lectures will be provided on the course page 

• The book “Principles of Proteomics” by R.M Twyman, Garland Science, ISBN: 9780815344728 (second edition) can be used as additional material. 

Students at KTH with a permanent disability can get support during studies from Funka:

Funka - compensatory support for students with disabilities

A, B, C, D, E, FX, F

• TEN1 - Written exam, 5.5 credits, Grading scale: A, B, C, D, E, FX, F
• ÖVN1 - Exercise, 1.0 credits, Grading scale: P, F
• ÖVN2 - Exercise, 1.0 credits, Grading scale: P, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

The examination consists of this course three parts: one practical and one oral exercise and a final oral exam.

The practical exercise is based on lab work conducted in groups. Each group will have one lab assistant to supervise the group. The goal is to generate and analyze data within a specified project. A written lab report summarizing the project will be handed in per group. Attendance and active participation are mandatory for all lab sessions. This is a group activity. Hence, all students will be evaluated as group members.

The oral exercise includes presenting your lab work to your peers. Each group prepares slides summarizing your results and observations in the context of the course content. Each group will also act as an opponent to another group, and all group members are expected to present and ask questions. Attendance and active participation are mandatory for the final workshop. This is a group activity. Hence all students will be evaluated as group members.

The oral exam is performed in groups of three students and consists of questions that aim to discuss the different topics within and around proteomics. Students are expected to show that they have obtained the knowledge according to the aims of the course. The students should also be able to express their opinions regarding various aspects of proteomics technologies. Opinions cannot be right or wrong, but the way the argumentation is presented will be evaluated. Each student will be evaluated individually and regardless of the other group members.

The assessment criteria is based on the intended learning outcomes:

The aim of the course is to provide the students with an introduction to current methods, challenges, and applications in the field of proteomics.  

After completion of the course, the student should be able to 

• describe and discuss the possibilities, advantages, complexity, and drawbacks of various proteomics technologies
• compare traditional methods with emerging technologies
• suggest suitable approaches for specified applications, motivate their choice
• speculate and argue about the future of proteomics technologies
• participate in scientific discussions regarding proteomics technologies
• critically evaluate scientific results

The words in bold are important for higher grades. In addition to describing the knowledge you have gained during the course, you also need to put the information into context and engage in a discussion where you apply the knowledge with your own critical thinking.

Complementory assignents will we offered for students missing mandatory elements.

Course activities and exam results will be reported within a week, provided that all assignments are submitted on time.

• All members of a group are responsible for the group's work.
• In any assessment, every student shall honestly disclose any help received and sources used.
• In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.