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Processing methods for differential analysis of LC/MS profile data
1Turku Centre for Biotechnology, Turku, Finland.
2VTT Biotechnology, Espoo, Finland.ORCID iD: 0000-0002-2856-9165
2005 (English)In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 6, article id 179Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i.e. broad screening of biomolecular components across multiple samples in order to elucidate the observed phenotypes and discover biomarkers. One of the major challenges in this domain remains development of better solutions for processing of LC/MS data.

RESULTS: We present a software package MZmine that enables differential LC/MS analysis of metabolomics data. This software is a toolbox containing methods for all data processing stages preceding differential analysis: spectral filtering, peak detection, alignment and normalization. Specifically, we developed and implemented a new recursive peak search algorithm and a secondary peak picking method for improving already aligned results, as well as a normalization tool that uses multiple internal standards. Visualization tools enable comparative viewing of data across multiple samples. Peak lists can be exported into other data analysis programs. The toolbox has already been utilized in a wide range of applications. We demonstrate its utility on an example of metabolic profiling of Catharanthus roseus cell cultures.

CONCLUSION: The software is freely available under the GNU General Public License and it can be obtained from the project web page at: http://mzmine.sourceforge.net/.

Place, publisher, year, edition, pages
BioMed Central, 2005. Vol. 6, article id 179
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:oru:diva-70895DOI: 10.1186/1471-2105-6-179ISI: 000231273200001PubMedID: 16026613Scopus ID: 2-s2.0-25444526868OAI: oai:DiVA.org:oru-70895DiVA, id: diva2:1345836
Available from: 2019-08-26 Created: 2019-08-26 Last updated: 2019-09-05Bibliographically approved

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Oresic, Matej

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CiteExportLink to record
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Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
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  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
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