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Mass spectrometry b...
Mass spectrometry based metabolomics for in vitro systems pharmacology : pitfalls, challenges, and computational solutions.
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- Herman, Stephanie (författare)
- Uppsala universitet,Klinisk kemi,Institutionen för farmaceutisk biovetenskap,Spjuth
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- Emami Khoonsari, Payam (författare)
- Uppsala universitet,Klinisk kemi
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- Aftab, Obaid, 1984- (författare)
- Uppsala universitet,Cancerfarmakologi och beräkningsmedicin
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- Krishnan, Shibu (författare)
- Uppsala universitet,Klinisk kemi
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- Strömbom, Emil (författare)
- Uppsala universitet,Cancerfarmakologi och beräkningsmedicin
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- Larsson, Rolf (författare)
- Uppsala universitet,Cancerfarmakologi och beräkningsmedicin
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- Hammerling, Ulf (författare)
- Uppsala universitet,Cancerfarmakologi och beräkningsmedicin
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- Spjuth, Ola, 1977- (författare)
- Uppsala universitet,Institutionen för farmaceutisk biovetenskap,Science for Life Laboratory, SciLifeLab,Spjuth
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- Kultima, Kim (författare)
- Uppsala universitet,Klinisk kemi
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- Gustafsson, Mats G (författare)
- Uppsala universitet,Cancerfarmakologi och beräkningsmedicin
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(creator_code:org_t)
- 2017-05-19
- 2017
- Engelska.
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Ingår i: Metabolomics. - : Springer Science and Business Media LLC. - 1573-3882 .- 1573-3890. ; 13:7
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https://doi.org/10.1...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- INTRODUCTION: Mass spectrometry based metabolomics has become a promising complement and alternative to transcriptomics and proteomics in many fields including in vitro systems pharmacology. Despite several merits, metabolomics based on liquid chromatography mass spectrometry (LC-MS) is a developing area that is yet attached to several pitfalls and challenges. To reach a level of high reliability and robustness, these issues need to be tackled by implementation of refined experimental and computational protocols.OBJECTIVES: This study illustrates some key pitfalls in LC-MS based metabolomics and introduces an automated computational procedure to compensate for them.METHOD: Non-cancerous mammary gland derived cells were exposed to 27 chemicals from four pharmacological classes plus a set of six pesticides. Changes in the metabolome of cell lysates were assessed after 24 h using LC-MS. A data processing pipeline was established and evaluated to handle issues including contaminants, carry over effects, intensity decay and inherent methodology variability and biases. A key component in this pipeline is a latent variable method called OOS-DA (optimal orthonormal system for discriminant analysis), being theoretically more easily motivated than PLS-DA in this context, as it is rooted in pattern classification rather than regression modeling.RESULT: The pipeline is shown to reduce experimental variability/biases and is used to confirm that LC-MS spectra hold drug class specific information.CONCLUSION: LC-MS based metabolomics is a promising methodology, but comes with pitfalls and challenges. Key difficulties can be largely overcome by means of a computational procedure of the kind introduced and demonstrated here. The pipeline is freely available on www.github.com/stephanieherman/MS-data-processing.
Ämnesord
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Nyckelord
- Batch effects
- Data handling
- Drug metabolism
- Mass spectrometry
- Metabolomics
- Bioinformatik
- Bioinformatics
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Herman, Stephani ...
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Emami Khoonsari, ...
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Aftab, Obaid, 19 ...
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Krishnan, Shibu
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Strömbom, Emil
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Larsson, Rolf
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Hammerling, Ulf
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Spjuth, Ola, 197 ...
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Kultima, Kim
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Gustafsson, Mats ...
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- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Data och informa ...
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och Bioinformatik
- Artiklar i publikationen
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Metabolomics
- Av lärosätet
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Uppsala universitet