CSI:FingerID: Best automated method in CASMI contest

CSI:FingerID participated in this year’s CASMI (Critical Assessment of Small Molecule Identification) contest for automated methods identifying compounds solely by mass spectral data without additional meta data (category 2). IOKR, the new prediction method within CSI:FingerID, won this category. Standard CSI:FingerId prediction method ranked 2nd best. For positive ionization, CSI:FingerID identified more than twice as much compounds than any other method.

We are pleased that SIRIUS and CSI:FingerID were successfully used by many other contestants in category 1.

You can try CSI:FingerID on http://www.csi-fingerid.org/. A commandline version as well as a user interface which allows batch processing of MS/MS data will be released soon. We will also integrate the new IOKR prediction method into the CSI:FingerID web interface.

Gastvorlesung Sebastian in Halle

Sebastian wird am Montag den 25.01.2016 zwei Vorlesungen zum Thema “Genome Rearrangements und Gene Clusters” an der Universität Halle halten.

Die Vorlesungen finden von 10:15 bis 12:00 Uhr in Seminarraum 1.30 sowie von 14:00 Uhr bis 15:15 Uhr in Seminarraum 0.04 des Institut für Informatik (Von-Seckendorff-Platz 1, Halle) statt.

Interessierte sind herzlich eingeladen.

Gastvorlesung Ivo Große

Ivo Große von der Universität Halle wird uns am 13. Januar besuchen und eine Gastvorlesung zum Thema Motif Finding und EM-Algorithmus halten – klassische Themen der Bioinformatik, die in Jena leider nicht mehr gelehrt werden.

Die Vorlesung findet am Mittwoch den 13. Januar von 9:30 bis 12:00 Uhr im Seminarraum 119, August-Bebel-Str. 4 statt.

Die Veranstaltung ist für alle Studierenden der Bioinformatik, insbesondere für alle Master-Studenten interessant. Alle Interessierten sind herzlich eingeladen.

We have published a paper in PNAS

Our paper “Searching molecular structure databases with tandem mass spectra using CSI:FingerID” has just appeared in the online issue of Proceedings of the National Academy of Sciences USA. Also see the press release by the Friedrich-Schiller-University Jena (here for German). The metabolite search engine CSI:FingerID is available from http://www.csi-fingerid.org/. This is joint work with Juho Rousu and his group at Aalto University (Finland).

SIRIUS 3.0 release

We present SIRIUS 3.0, a java-based software for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry.
SIRIUS uses isotope pattern analysis for detecting the molecular formula and further analyses the fragmentation pattern of a compound using fragmentation trees.

The version 3.0 is a complete rewrite of our previous software. It uses faster algorithms for the fragmentation tree computation and a revised scoring based on Bayesian statistics.

A command line tool is available here. We will add a graphical user interface soon.