Identifying unknown metabolites using fragmentation trees

Lecturer : 
Prof. Sebastian Böcker, Friedrich Schiller University, Jena, Germany
Event type: 
Guest lecture
Event time: 
2013-08-20 14:15 to 15:00
Aalto University, Computer Science Building, lecture hall T2


The structural elucidation of organic compounds in complex biofluids
and tissues remains a significant analytical challenge.  For mass
spectrometry, the manual interpretation of collision-induced
dissociation (CID) mass spectra is cumbersome and requires expert-
knowledge, as the fragmentation mechanisms of ions formed from small
molecules is not completely understood.  The automated identification
of compounds is generally limited to searching databases in spectral

In my talk, I will present a method for interpreting fragmentation
spectra by computing fragmentation trees: These establish not only the
molecular formula of the compound and all fragment ions, but also the
dependencies between fragment ions.  Second, I will present a method
for the automated comparison of such trees, and show how to use this
method for clustering unknown compounds and for searching unknowns not
in any database (Fragmentation Tree Basic Alignment Search Tool, FT-
BLAST). I will also report our recent progress on the problem.

About the speaker:

Sebastian Böcker is a full professor at the Friedrich Schiller
University Jena, and leader of the Chair for Bioinformatics at the
Institute for Computer Science.  Previous to his academic career, he
has worked for three years in industry.  He has a long-standing
expertise in bioinformatics, algorithmics, and combinatorial
optimization.  He is author of more than 95 refereed papers.  He is
particularly interested in computational methods for mass
spectrometry, phylogenetics and supertree methods, gene cluster
analysis, and algorithm development for computationally hard problems
in bioinformatics.

Last updated on 14 Aug 2013 by Antti Ukkonen - Page created on 14 Aug 2013 by Antti Ukkonen