Our paper “Significance estimation for large scale metabolomics annotations by spectral matching” (joined work with the group of Pieter Dorrestein) has finally appeared in Nature Communications; you can find it here.
Friedrich-Schiller-Universität Jena, Fakultät für Mathematik und Informatik
Our paper “Significance estimation for large scale metabolomics annotations by spectral matching” (joined work with the group of Pieter Dorrestein) has finally appeared in Nature Communications; you can find it here.
CASMI (Critical Assessment of Small Molecule Identification) 2017 results are finally out! Kai participated with SIRIUS/CSI:FingerID, and won categories 1 (Best Structure Identification on Natural Products), 2 (Best Automatic Structural Identification – In Silico Fragmentation Only), and 4 (Best Automatic Candidate Ranking). He did not participate in category 3.
For category 4 (in silico methods for searching in molecular structure databases), CSI:FingerID correctly identified 66 of 198 compounds (33.3%). This is more than 6-fold of what the best non-CSI:FingerID contestant reached. (Submissions containing “IOKR” in their name, correspond to different variants of the Input Output Kernel Regression version of CSI:FingerID.)
Unfortunately, CASMI 2017 data did not include isotope patterns. It appears that in many cases, SIRIUS was not able to find the correct molecular formula among the top candidate. This resulted in several cases where the correct structure was excluded due to the “wrong” molecular formula. We will investigate how many compounds would have been correctly identified if isotope pattern data would have been available.
Kai and Marcus will give talks at Metabolomics conference 2017 in Brisbane on Wed, June 28th.
Kai will talk about CANOPUS, the new tool for compound category prediction. Marcus will discuss ZODIAC, a method for comprehensive molecular formula identification on complete LC/MS runs with tandem mass spectra.
The CSI:FingerID web service has just passed the mark of processing data from 500,000 query compounds — congratulations to CSI:FingerID, and thank you for your interest in our tools! (Be reminded that CSI:FingerID should be accessed via the SIRIUS application, not via the web page.)
Our new version, Sirius 3.5, comes with several advancements. Download and use it here.
We have a new overview tab for CSI:FingerID hits which displays results of structure search for multiple molecular formulas.
You can examine the predicted fingerprint of each compound (and molecular formula) independently of any database.
We now offer the possibility to create and search in custom structure databases.
Besides, we have a new bayesian networks scoring function for CSI:FingerID which considers dependencies between different molecular properties.
This and much more.
A new Sirius version is available. We included new features to enable a more intuitive workflow. We hope you’ll like it. Download and use it here.
We provide element prediction using isotope pattern. CSI:FingerID now predicts more molecular properties which improves structure identification.
Besides we fundamentally changed the structure of the result output generated by the command line tool to its final version. This means you might have to adjust your workflow.
Today, Kerstin was awarded the “Wissenschaftspreis für anwendungsorientierte Abschlussarbeit” (scientific award for application-oriented thesis) from the Wirtschaftsförderungsgesellschaft mbH and the FSU Jena, for her PhD thesis “Small molecules: From mass spectral fragmentation data to structural elucidation”. Congratulations!
Sebastian will give a talk on CSI:FingerID and SIRIUS at the OpenMS user meeting 2016 in Tübingen, 21-23 September 2016.
Sebastian will give a talk at the de.NBI Summer School 2016: From Big Data to Big Insights (Dagstuhl, 26-30 September 2016).
SIRIUS+CSI:FingerID is no available for Mac. You can download it here. A few highlights of the new version:
Don’t hesitate to give us your feedback, report bugs or suggesting new features. Just write to
SIRIUS+CSI:FingerID leaves the alpha state. You can download it here. A few highlights of the new version:
Don’t hesitate to give us your feedback, report bugs or suggesting new features. Just write to
The CASMI winner methods SIRIUS and CSI:FingerID are now available as a user interface. This allows users to batch process their spectra; which was not possible for the web application of CSI:FingerID.
You can try an early alpha version of SIRIUS+CSI:FingerID here.
Within the next three weeks we will release the final 3.1.4 version. Please report bugs to .
Kai, Franziska and Marcus are visiting the Metabolomics in Dublin from Monday, 27 June 2016 to Thursday, 30 June 2016.
Franziska is giving a talk on the Significance of metabolite identifications from searching mass spectral libraries.
Marcus will speak about our new Confidence score for CSI:FingerID identifications.
Kai will present the new SIRIUS 3.2 release.
Wir sind dabei, beim MINT-Schülerkongress 2016 des Schülerforschungszentrums Nordhessen in Kassel.
Alle weiteren Infos findet ihr hier.
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.
Das German Network for Bioinformatics Infrastructure (de.NBI) läd ein zur de.NBI Summer School 2016 unter dem Motto “From Big Data to Big Insights: Computational methods for the analysis and interpretation of mass-spectrometric high-throughput data”
Interessenten können sich noch bis zum 1. Juni bewerben.
Mehr Infos gibt es hier.
Bertram and Franziska are visiting the 31st TBI Winterseminar in Bled from Sunday, 14 Feb 2016 to Friday, 19 Feb 2016. Bertram is giving a talk on Transcriptomics in Cyanobacteria.
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.
Ab sofort wird Franziska auf ihrem Blog wöchentlich über Forschungsfelder, aktuelle Publikationen und Karrieremöglichkeiten aus der Bioinformatik berichten.