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SmartPeak automates targeted and quantitative metabolomics data processing

View ORCID ProfileSvetlana Kutuzova, Pasquale Colaianni, View ORCID ProfileHannes Röst, View ORCID ProfileTimo Sachsenberg, View ORCID ProfileOliver Alka, View ORCID ProfileOliver Kohlbacher, View ORCID ProfileBo Burla, View ORCID ProfileFederico Torta, View ORCID ProfileLars Schrübbers, View ORCID ProfileMette Kristensen, View ORCID ProfileLars Nielsen, View ORCID ProfileMarkus J. Herrgård, View ORCID ProfileDouglas McCloskey
doi: https://doi.org/10.1101/2020.07.14.202002
Svetlana Kutuzova
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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  • ORCID record for Svetlana Kutuzova
Pasquale Colaianni
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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Hannes Röst
2University of Toronto, Donnelly Centre for Cellular & Biomolecular Research, 160 College St. Toronto, ON, Canada
7Department of Molecular Genetics, University of Toronto, Toronto, Canada
8Department of Computer Science, University of Toronto, Toronto, Canada
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Timo Sachsenberg
3Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
9Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
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Oliver Alka
3Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
9Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
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Oliver Kohlbacher
3Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
9Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
10Biomolecular Interactions, MPI for Developmental Biology, Tübingen, Germany
11Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
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Bo Burla
4Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
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Federico Torta
5Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
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  • ORCID record for Federico Torta
Lars Schrübbers
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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  • ORCID record for Lars Schrübbers
Mette Kristensen
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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  • ORCID record for Mette Kristensen
Lars Nielsen
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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  • ORCID record for Lars Nielsen
Markus J. Herrgård
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
6BioInnovation Institute, Ole Maaløes Vej 3, 2830 Copenhagen N, Denmark
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Douglas McCloskey
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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  • ORCID record for Douglas McCloskey
  • For correspondence: domccl@biosustain.dtu.dk
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Abstract

SmartPeak is an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of CE-, GC- and LC-MS(/MS) data, and HPLC data for targeted and semi-targeted metabolomics, lipidomics, and fluxomics experiments.

Highlights

  • Novel algorithms for retention time alignment, calibration curve fitting, and peak integration

  • Enables reproducibility by reducing operator bias and ensuring high QC/QA

  • Automated pipeline for high throughput targeted and/or quantitative metabolomics, lipidomics, and fluxomics data processing from multiple analytical instruments

  • Manually curated data set of LC-MS/MS, GC-MS, and HPLC integrated peaks for further algorithm development and benchmarking

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/dmccloskey/SmartPeak2

  • https://www.ebi.ac.uk/metabolights/MTBLS1786

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 15, 2020.
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SmartPeak automates targeted and quantitative metabolomics data processing
Svetlana Kutuzova, Pasquale Colaianni, Hannes Röst, Timo Sachsenberg, Oliver Alka, Oliver Kohlbacher, Bo Burla, Federico Torta, Lars Schrübbers, Mette Kristensen, Lars Nielsen, Markus J. Herrgård, Douglas McCloskey
bioRxiv 2020.07.14.202002; doi: https://doi.org/10.1101/2020.07.14.202002
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SmartPeak automates targeted and quantitative metabolomics data processing
Svetlana Kutuzova, Pasquale Colaianni, Hannes Röst, Timo Sachsenberg, Oliver Alka, Oliver Kohlbacher, Bo Burla, Federico Torta, Lars Schrübbers, Mette Kristensen, Lars Nielsen, Markus J. Herrgård, Douglas McCloskey
bioRxiv 2020.07.14.202002; doi: https://doi.org/10.1101/2020.07.14.202002

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