West Coast Metabolomics Center Summer/Winter Course Slides 2012-2017

Tobias Kind - Creative Commons by Attribution License (CC-BY)

  • Course 1: General Introduction [PDF] [PPT]
  • Course 2: Mass spectral and molecular data handling [PDF] [PPT]
  • Course 3: Mass spectral and molecular database search [PDF] [PPT]
  • Course 4: Mass Spectrometry Tools & Concepts [PDF] [PPT]
  • Course 5: Concepts for GC-MS [PDF] [PPT]
  • Course 6: Concepts for LC-MS [PDF] [PPT]
  • Course 7: Prediction and simulation of mass spectra [PDF] [PPT]
  • Course 8: Search of electron ionization (70 eV) mass spectra with the NIST MS Search GUI [PDF]
  • Course 9: Search of MS/MS files with the NIST MS Search GUI [PDF]
  • Course 10: Batch processing of multiple MS/MS files and qualitative compound annotation [PDF]

Mass Spectrometry course by Prof. Julie Leary Current: CHE 241C - Spring 2009 - Mass Spectrometry - CRN 26608 (see full UC Davis Course System) MWF 1210-1300 WELLMN 229; Monday and Friday will be chalkboard teaching and Wednesdays computer class

The computer class is scheduled on Feb 11 and will be at 2020 LSB (MAP) the new Science Laboratory Building across Briggs Hall. The Friday class on Feb 13th is as usual in CHE 241C. Please tell your fellow students and friends. Requirements: Your UC Davis Kerberos loginHistoric: CHE 241 - Spring 2008 - CRN 16583 (see full UC Davis course system classes.ucdavis.edu)

I will start teaching on Feb 22, 25, 27, 29, March 3, 5, 7, 10, 12 and March 14 2008. Last day will be class evaluation.


This is a proxy class. I will focus in the second part on combining mass spectrometry data with cheminformatics and chemometrics. Fully linked Powerpoint slides will be available here before each class. DOI linked reading lists will be available in the PowerPoint, homework tasks will be included.

(A) Attendees have to have access to own computer (mostly WINDOWS) and UC Davis Internet (for literature) and possibly have to install programs or otherwise will have to ask us for help.

(B) Please prepare yourself by going trough this list of program and databases which include structure elucidation concepts with FT-MS, MS/MS, GC-MS, LC-MS. Trying out some of the programs and databases will give a slight advantage and better understanding [LINK]

(C) Please familiarize yourself with concepts which were already introduced by Prof. Leary in the first part of the class. Please follow the Teaching on the Seven Golden Rules, which include the concepts of Accurate Mass, Accurate Isotopic Abundances, Mass Resolution, Nitrogen Rule, Ring Double Bond Equivalents, MS/MS Fragmentation, Isotopic Pattern Generators, Formula Generators, Database Annotations, Isomer Generation and the Molecular Formula Space an the Molecular Isomer Space. Each section has links to literature or linked files which are interesting to read. This will give a slight advantage and better understanding during the course. Thank you!

Teaching PPT slides (Due to some bugs in MS Office you may not see all pictures; see MHT or PDF):

Comment: These slides are deprecates and kept for historical reasons, please refer for to the updated slides on top.


Graduate level course MCB221b - Mechanistic Enzymology (December 2007) + (Winter 2010)

by Prof. Enoch Baldwin and Prof. Oliver Fiehn; Invited lectures:


There is a publication about the teaching approach in our course using virtual machines, see here: Kind T, Leamy T, Leary JA, Fiehn OSoftware platform virtualization in chemistry research and university teaching. Journal of Cheminformatics 2009, 1:18 doi:10.1186/1758-2946-1-18 [LINK] [PDF] [PREPRINT]



You can re-use all the teaching slides under the Creative Commons Licence (CC-by). Reference: Tobias Kind - UC Davis Genome Center - Fiehnlab Metabolomics This may not include pictures from WikiMedia and Office and other mentioned material.