Biomedical Engineering Reference
In-Depth Information
traps (Orbitrap, Qtrap) have provided the researcher with unprecedented
resolving power and potential.
In some ways it could be argued that the technology has moved faster
than our ability to deal with the data. Despite such high-resolution
instruments being available for several years, even instrument vendors'
software has struggled to keep pace with the potential abilities these
instruments provide. In addition, the modern spectrometer places a
huge strain on the computing hardware both in terms of storage and
processing power. Our ability to process and make sense of such large
data sets relies on cutting edge data visualisation and multivariate
statistical methods.
Possibly for these reasons there have been a large number of open
source projects started by researchers in mass spectrometry, chemometrics,
metabolomics and proteomics. It is a rapidly developing area with many
new innovations still to be made and one where collaboration is essential.
We are moving into an age of research where no one person can possibly
keep up with all the skills required. Instead communication and
networking skills are becoming as important as scientifi c knowledge.
Fortunately, the open source software community is an excellent forum
for such collaborations.
In this chapter a few of these open source tools will be demonstrated.
4.2 A short mass spectrometry primer
As some readers of this topic may be unfamiliar with mass spectrometry,
here is a short explanation. (Mass spectrometry experts may wish to skip
this section.)
A mass spectrometer can be described simply as a device that separates
ions based on their mass to charge ratio. It is frequently used as a detector
as part of a chromatography system such as high pressure liquid
chromatography (HPLC), gas chromatography or used alone with
samples being introduced from surfaces using laser desorption
(MALDI) or directly from air (DART). Chemical samples are therefore
introduced to the mass spectrometer as solutions, gases or vapours. The
introduced substances are then ionised so that they may be defl ected by
electrostatic or magnetic fi elds within the spectrometer. Ions with different
masses are defl ected to different extents, so, by varying the defl ection
strength, a range of mass/charge ratios may be determined. The resulting
plot of the molecular weight versus ion abundance is known as a mass
spectrum.
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