SIRIUS+CSI:FingerID for Mac OSX

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SIRIUS+CSI:FingerID is no available for Mac. You can download it here. A few highlights of the new version:

  • Searching your tandem mass spectra in molecular databases using CSI:FingerId
  • Restrict the SIRIUS molecular formula identification to formulas appearing in molecular databases – or search through the whole space of possible formulas. It’s up to you.
  • Sort you identification results by confidence such that more reliable identifications (e.g. from high quality spectra or easy recognizable compounds) are separated from bogus identifications.
  • Predict structural features and substructures from tandem mass spectra and visualize them in your candidate structure list.

Don’t hesitate to give us your feedback, report bugs or suggesting new features. Just write to sirius-devel@listserv.uni-jena.de

SIRIUS+CSI:FingerID release

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SIRIUS+CSI:FingerID leaves the alpha state. You can download it here. A few highlights of the new version:

  • Searching your tandem mass spectra in molecular databases using CSI:FingerID
  • Restrict the SIRIUS molecular formula identification to formulas appearing in molecular databases – or search through the whole space of possible formulas. It’s up to you.
  • Sort you identification results by confidence such that more reliable identifications (e.g. from high quality spectra or easy recognizable compounds) are separated from bogus identifications.
  • Predict structural features and substructures from tandem mass spectra and visualize them in your candidate structure list.

Don’t hesitate to give us your feedback, report bugs or suggesting new features. Just write to sirius-devel@listserv.uni-jena.de

SIRIUS+CSI:FingerID alpha release

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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 sirius-devel@listserv.uni-jena.de.

Meet us at Metabolomics 2016

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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.

CSI:FingerID: Best automated method in CASMI contest

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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

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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

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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

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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).

Meet Sebastian at Metabolomics 2015

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Sebastian will attend the Conference of the Metabolomics Society 2015 in San Franciso, and give a talk on “Searching molecular structure databases with tandem mass spectra using CSI:FingerID”. On Tuesday after 6 pm, Steffen Neumann and Sebastian will head the BoF meeting on Computational Mass Spectrometry.

Kinderuni am Freitag 19. Juni

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Am Freitag 19. Juni 2015 wird Sebastian im Rahmen der KinderUni Jena einen Vortrag zum Thema “Auch Computer müssen aufräumen” halten. Start ist um 16:00 Uhr, Veranstaltungsort ist der Hörsaal 7 in der Carl Zeiss Straße 3 (neben der Mensa).