Course Identification

Analysis of Small Molecules: Metabolic Profiling and Mass Spectrometry Imaging

Lecturers and Teaching Assistants

Prof. Asaph Aharoni, Dr. Ilana Rogachev, Dr. Herbert Uwe Heinig, Dr. Sergey Malitsky

Course Schedule and Location

Second Semester
7-18 of May: lectures and labs,

Field of Study, Course Type and Credit Points

Life Sciences: Laboratory; Elective; Regular; 1.00 points


7-18 of May: lectures and labs
24th of May: student?s presentations





Language of Instruction


Attendance and participation


Grade Type

Pass / Fail

Grade Breakdown (in %)


Evaluation Type


Scheduled date 1


Estimated Weekly Independent Workload (in hours)



Low molecular weight biological molecules or so called ‘metabolites’ are vital for viability and fitness of all living creatures. Separation, detection, identification and quantification of hundreds of thousands of metabolites possessing endless structures is a great challenge, requiring ample expertise in analytical chemistry. Yet, proficiency in such methodologies is critically needed in many labs, both biology and chemistry oriented ones. This course will offer a unique opportunity to gain fundamental knowledge in using analytical chemistry for the interrogation of metabolites in any given organism.

Mass spectrometry (MS) is a core technology providing the capacity to detect, quantify and identify metabolites. The course will provide both theoretical background as well as practical, hands-on experience with respect to analyzing small molecules in biological tissues. Course attendees will get acquainted with chromatography coupled to mass spectrometry, and mass spectral imaging, where the main focus will be done on Gas Chromatography-MS (GC-MS) and Mass Spectrometry Imaging (MSI) technologies. The practical part will be carried out in small groups and will include hands-on activity that will cover sample preparation, analytical runs on GC-MS and MSI systems as well as raw data analysis and downstream data processing. The course is complementary to the first semester practical course entitled “Analysis of Small Molecules: Targeted and Non-Targeted Assays” that is largely focused on LC-MS analysis.

Theoretical part


7th of May:

Introduction to the course – 9:15-10:00 – Asaph Aharoni

Introduction to metabolite separation methods (1st part) – 10:05-11:00 – Sergey Malitsky- room 4


8th of May:

Introduction to metabolite separation methods (2nd part) – 9:15-11:00 – Sergey Malitsky- room 4


9th of May:

Introduction to mass spectrometry (1st part) – 9:15-11:00– Ilana Rogachev- room 4


10th of May:

Introduction to mass spectrometry (2nd part) – 9:15-11:00– Ilana Rogachev- room 4


11th of May:

Mass Spectrometry Imaging – 9:15-11:00 – Herbert Uwe Heinig

e- room 5

14th of May:

GC-MS analysis – 9:15-11:00 – Sergey Malitsky- room 4



Practical (hands-on) part

15 – 18 of May (4 days), 11:15-16:15 each day (Sergey Malitsky and Herbert Uwe Heinig)

Location of practical part will be announced later


Student’s presentations:

24th of May, 11:00-14-00 hours (all mentors)- room 4

Learning Outcomes

Upon successful completion of this course students should be able to:

  1. Understand the basics of mass spectrometry.
  2. Understand the basics of GC-MS and MSI technologies.
  3. Prepare samples for the different methods of analysis, appreciate data collection and analysis.
  4. Discuss the various applications, limitations and restrictions of the various methods

Reading List