New Statistical Algorithms for the Analysis of Mass - FU Berlin, FB MI ...

Chapter 7
Related Work
In this chapter we will give a brief overview of other projects related to this
thesis. Since related algorithms and concepts have been already discussed
in the relevant chapters we will focus here on whole pipelines or frameworks
for the analysis of protein MS TOF data. These pipelines can be roughly
categorized into three groups:
1. Collection of stand alone tools for data processing (e.g. peak picking,
identification or quantitation)
2. Integrated software platforms that offer data processing tools and data
management functionality, usually providing a graphical user interface
that allows for the assembly and execution of workflows. Since these
platforms run on a single machine they are not well suited for the analysis
of very large datasets.
3. Software platforms that offer data processing, data management and
support distributed computation of their algorithms. Opposed to the
previous category these frameworks are also well suited to handle very
large datasets.
Interestingly, the shift from development of stand-alone tools to integrated
platforms has only become widespread since increase in data volume became
an issue. Still, most of these systems address only a part of the pipeline
described in this thesis. High-throughput laboratories such as the Seattle
Proteome Center (Trans-Proteomics Pipeline 1 , TPP (Kiebel et al., 2006)), the
Institute of Molecular Systems Biology at ETH Zürich (Superhirn, (Mueller
et al., 2007)) or the Institute of Biomedical Engineering at Imperial College
London (ProteomeGRID, (Dowsey et al., 2004)) have developed significant
platforms with similar functionality. However, none of them provides the
full range of the discovery process lifecycle including distributed computing
support as our platform does.
Other software packages such as mzMine 2 by Turku Centre for Biotechnology
(Katajamaa et al., 2006), OpenMS 3 by Freie Universität Berlin (Kohlbacher
et al., 2007) or XCMS 4 by Scripps Center for Mass Spectrometry (Smith et al.,
2006) are not complete platforms (yet) since there is no graphical user interface,
workflow or data management functionality.
1 http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
2 http://mzmine.sourceforge.net/
3 http://www.openms.de
4 http://metlin.scripps.edu/download/
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