Matej Oresic talks with
ScienceWatch.com 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
Journal: BIOINFORMATICS
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?
"With the help of MZmine we
may help address and even solve some of the
important healthcare issues of today and
tomorrow."
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