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February 2008

Matej Oresic talks with and answers a few questions about this month's Fast Breaking Paper in the field of Computer Science.
Article Title: MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data
Authors: Katajamaa, M;Miettinen, J;Oresic, M
Volume: 22
Issue: 5
Page: 634-636
Year: MAR 1 2006
* VTT Tech Res Ctr Finland, Espoo, Finland.
* VTT Tech Res Ctr Finland, Espoo, Finland.
(addresses may have been truncated; see full article)

  Why do you think your paper is highly cited?

This paper is the first that offers both open source and vendor-independent solutions for the mass spectrometry-based (MS) data processing pipeline, with the primary application areas being metabolomics and proteomics. Due to its open source distribution it is also easily expandable and enables others to contribute new methods for specific stages of MS data processing. This is not possible with commercial solutions, neither by most of the other software previously developed by academic groups.

  Does it describe a new discovery, methodology, or synthesis of knowledge?

The paper describes a new software, MZmine, which also includes some new methods such as those used for peak detection and spectral alignment and also for early-stage processing of mass spectrometry. MZmine is thus a collection of established, as well as new, methods for MS-based metabolomics and proteomics applications, and it is easily expandable due to its open source license.

  Would you summarize the significance of your paper in layman’s terms?

The paper introduces the open source software MZmine, which enables researchers to extract raw data from metabolomic or proteomic analyses, and processes the data through multiple stages to obtain data that can be analyzed and interpreted within the context of application and experiment design (e.g., biological problem).

  How did you become involved in this research, and were there any problems along the way?

Development of this software is not the main area of our group’s research. The software was developed due to our own metabolomics research needs and obvious lack of flexible software solutions in the area of metabolomics and proteomics. We thus decided to develop a package that would be widely available to other researchers as well, and along the way also developed a few new solutions for the specific problems of data processing.

  Where do you see your research leading in the future?

We will continue improving MZmine, particularly in terms of newer methods which improve the quality of data processing, as well as facilitate interpretation of data by connectivity with various life science databases. Above all, we will continue using MZmine in a large number of metabolomics projects, e.g., we are going to apply MZmine in search of early metabolic biomarkers for breast cancer, atherosclerosis, and type 1 diabetes mellitus.

  Do you foresee any social or political implications for your research?

With the help of MZmine we may help address and even solve some of the important healthcare issues of today and tomorrow. With the number of users of MZmine increasing, it is likely we will contribute directly to the discovery of solutions for many other important research questions of social and perhaps also political importance.

Matej Oresic, PhD
Professor (Systems Biology and Bioinformatics)
VTT Technical Research Centre of Finland
Espoo, Finland

2008 : February 2008 - Fast Breaking Papers : Matej Oresic - February 2008
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