SIRIUS 4.4 is coming soon!

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It’s been a while since SIRIUS 4 received its last update. We are excited to announce that SIRIUS 4.4 is coming soon.
It comes with many new features, e.g.:

  • Project-Space: A standardized persistence layer shared by CLI and GUI that makes both fully compatible.
  • Redesigned Command Line Interface: SIRIUS is now a toolbox that contains different sub-tools that can be combined to “tool-chains”.
  • New (and newly integrated) tools:
    • ZODIAC: Improve Molecular Formula Identifications by re-ranking SIRIUS molecular formula annotations using Bayesian statistics. ZODIAC optimizes annotations on a whole dataset taking advantage of the fact that compounds usually co-occur in a network of derivatives.
    • PASSATUTTO: Is now part of SIRIUS and allows you to generate dataset specific decoy spectral libraries from computed fragmentation trees.
    • lcms-align: SIRIUS supports mzML/mzXML format to process whole LC-MS/MS runs. The lcms-align preprocessing tool performs feature detection and feature alignment based on the available MS/MS spectra.
    • Other handy standalone tools, e.g. compound similarity calculation.

To provide user friendly but also flexible and customizable access to the different tools we completely redesigned the command line interface (CLI).
We know that this might break your workflows and therefore we provide you an early access version of the CLI that can be used for testing and adapting your workflows:
https://bio.informatik.uni-jena.de/repository/list/dist-snapshot-local/de/unijena/bioinf/ms/sirius/4.4.0-SNAPSHOT/
You will also find an updated version of the manual which is still work-in-progress but contains already an updated section on the new CLI.

No worries, even when SIRIUS 4.4. will be released (as soon as the GUI is ready) version 4.0.1 will still be available for some time.

If you find bugs or have any feedback feel free to open an issue on the SIRIUS GitHub repository or contact us via .

Preprint of ZODIAC now on bioRxiv

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A preprint of our paper “ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules.” is now available: https://doi.org/10.1101/842740

ZODIAC takes advantage of the fact that an organism produces related metabolites. ZODIAC builds upon SIRIUS and reranks molecular formula candidates, optimizing annotations on whole datasets. By applying ZODIAC to multiple datasets we greatly increased the number of correct annotations and identified novel molecular formulas which are not present even present in PubChem.

ZODIAC will be made available in an upcoming release of the SIRIUS software.

 

 

Meet us at GCB 2019

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Sebastian, Kai, Martin and Marcus are attending the German Conference on Bioinformatics in Heidelberg. We look forward to a great conference.

New version of Lecture Notes on Algorithmic MS

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I have just uploaded a new version (0.8.3) of the Lecture Notes on Algorithmic Mass Spectrometry. As expected, I did not have too much time to work on it (them?) during lecture time, which is luckily over now. It is a lot of small improvements. Also, Magnus Palmblad was so kind and had an expert look through the isotope pattern sections. Unfortunately, the stuff that was missing from the previous version, is still missing now…

Meet us at ISMB 2019

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Meet Markus at the ISMB/ECCB 2019 in Basel.

On Tuesday, Markus will give a talk about “SIRIUS 4: turning tandem mass spectra into metabolite structure information”.
There is also a corresponding poster in Session A (J-06) which will be presented on Tuesday 6:00pm-8:00pm.

Meet us at Metabolomics 2019

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Meet Marcus and Sebastian at the conference of the Metabolomics Society 2019.

On Monday and Tuesday, Marcus will present a poster (539) about SIRIUS 4 and turning tandem mass spectra into metabolite structure information.

DFG project on retention time/order prediction granted

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The Deutsche Forschungsgemeinschaft has granted a project on retention time and order prediction for liquid chromatography. This is a joint project with Michael Witting, Helmholtz Zentrum München.

The idea of the project is to integrate retention times from liquid chromatography into the SIRIUS/CSI:FingerID identification pipeline. Literally hundreds of papers have been published on the topic of retention time prediction, but all of them fail to provide predictions that are transferable across chromatography conditions and compound classes; see Héberger’s review (Journal of Chromatography A, 2007) where he speaks rather frankly about the malpractices of publishing such RT-prediction methods. On the other hand, retention times can indeed be used to further boost CSI:FingerID’s identification performance. Also, transferable retention prediction is not impossible, as we have shown here. The trick is not to try to predict retention time (which is extremely dependent on instrument parameters etc) but rather retention order.

We are searching for a qualified and motivated PhD student who wants to accept this challenge. (S)he should be knowledgeable in machine learning and preferably also bioinformatics in general; biochemistry knowledge is clearly also a plus. We believe that this can be the next big thing to further push CSI:FingerID’s performance. Please contact Sebastian or Kathrin in case you are interested and qualified.

IMPRS application call for PhD students

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The International Max Planck Research School at the Max Planck Institute for Chemical Ecology in Jena is looking for PhD students. One of the projects is from our group on “making SIRIUS and CSI:FingerID GCMS-ready”. Deadline is May 24, 2019.

SIRIUS and CSI:FingerID are the best-of-class tools for MS-based compound identification in metabolomics, natural products and related fields. More than one million compound queries have been submitted to our web service, from over 3000 users and 47 countries. See our recent publication in Nature Methods (Dührkop et al., 2019).

Currently, our tools can only process tandem mass spectrometry data; extending them to Gas Chromatography Electron Ionization appears natural, but comes with numerous challenging problems from algorithmics and machine learning. This will be done in cooperation with the group of Georg Pohnert, see his recent publication in Nature (Thume et al., 2018).

We are searching for motivated candidates from bioinformatics, machine learning, cheminformatics and/or computer science who want to work in this exciting, quickly evolving interdisciplinary field. Please contact Sebastian Böcker in case of questions.

Half a position is being paid by the IMPRS; this will be supplemented by funding from our chair to 2/3 TV-L E13. (Note that the cost of living in East Germany is still considerably lower than in West Germany.) Jena is a beautiful city and wine is grown in the region: https://www.youtube.com/watch?v=DQPafhqkabc.

IMPRS: http://imprs.ice.mpg.de/
MPI-CE: http://www.ice.mpg.de/
SIRIUS & CSI:FingerID: https://bio.informatik.uni-jena.de/software/sirius/
Literature: https://bio.informatik.uni-jena.de/publications/ and https://bio.informatik.uni-jena.de/textbook-algoms/

Jena: https://www.google.de/search?q=jena&tbm=isch&
https://www.study-in.de/en/discover-germany/german-cities/jena_26976.php
https://www.google.com/search?q=jena&tbm=isch

Our SIRIUS 4 paper is now available at Nature Methods

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We are happy to announce that our paper “SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information” is now available online at Nature Methods.

  • K. Dührkop, M. Fleischauer, M. Ludwig, A. A. Aksenov, A. V. Melnik, M. Meusel, P. C. Dorrestein, J. Rousu, and S. Böcker, “Sirius 4: Turning tandem mass spectra into metabolite structure information,” Nature Methods, doi 10.1038/s41592-019-0344-8, 2019.

View-only access to the paper is available here.

Dagstuhl seminar on Computational Metabolomics filling up quickly

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Another Dagstuhl seminar on Computational Metabolomics will be held in January 2020. The seminar is filling up quickly: Less than a month ago, invitations have been send out; but 25 people have already accepted the invitation! That is a lot, considering that it is still 10 months to go.

The title of the Dagstuhl seminar is “Computational Metabolomics: From Cheminformatics to Machine Learning“; it will be organized by Corey Broeckling, Emma Schymanski, Nicola Zamboni and myself. Unfortunately, it is invitation only. Two Dagstuhl seminars on related topics (Seminar 15492 in Nov/Dec 2015 and Seminar 17491 in Dec 2017) were already very successful.

Hope that we have a jolly good time in Dagstuhl!

SIRIUS and CSI:FingerID user meeting?

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With SIRIUS and CSI:FingerID gathering interest in the community, we are thinking about a SIRIUS and CSI:FingerID user meeting (a SIRIUS user meeting, so to say) in Jena. This would be a 2-3 day come-together with the possibility to show what your are doing with our tools, discuss with the developers, give us feedback on what is SIRIUSly needed etc. We are open to suggestions.

But most importantly: Are you interested in such a meeting? Would you come to Jena for 2-3 days? When would be a good time? (September is the default, but this is usually packed.)

In case you are interested, please let us know. You can leave your comment below, but please also send an email to the SIRIUS email address.


SIRIUS 4.0.1 released

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A new version of SIRIUS 4 is available for download.
SIRIUS 4.0.1 brings many bugfixes, user interface polishing and improved stability of the CSI:FingerID backend.

  • SIRIUS 4.0.1 now supports JAVA 9 and higher
  • The structures used to train CSI:FingerID are now available via the web service:
    • https://www.csi-fingerid.uni-jena.de/webapi/trainingstructures.csv?predictor=pos
    • https://www.csi-fingerid.uni-jena.de/webapi/trainingstructures.csv?predictor=neg

See our changelog for further details .

You can download SIRIUS with CSI:FingerID here.