Biology Reference
In-Depth Information
Filtering is one of the basic operations, and functionalities are neces-
sary to carry out a complete LC/MS study. Usually, this operation
removes peaks with weaker intensities (e.g. background noise) or high
spikes constant in time (e.g. chemical noise such as column contami-
nants) so as to reduce the complexity of spectra and facilitate peak detec-
tion. Peak detection involves looking for the monoisotopic peaks (also
called the deisotoping procedure) and determining the states of the ion
charge. Finally, isotopic peaks of the same corresponding mass value are
clustered into one single peak signal. In fact, this procedure selects the
peaks of interest from the enormous quantity of data.
Ideally, the same molecules analyzed in the same LC/MS platform
would have the same retention time, molecular weight, and signal intensity.
However, due to experimental variations, this is not always the case.
While m / z values depend on mass accuracy and the resolution of the
mass spectrometer, the retention times largely depend on the analytical
method used. Peaks from the same compound or peptide match fairly
close in m / z values, but the retention times between the runs can vary
significantly. The peak alignment operation corrects these variations and
finds corresponding peaks across different LC/MS runs. Once runs
are aligned, they can be compared and statistically analyzed in order to
find differentially expressed proteins and peptides, and to quantify these
differences.
Similarly to 2-DE gel analysis software, due to the large amount of
data generated through LC/MS experiments, LC/MS image analysis
software does not usually run through Web interfaces or on a remote
basis. All tools are available as stand-alone versions that have to be
installed and run locally.
MSight , 14 a software developed by the PIG, is a free downloadable
software available through the ExPASy 15 server. Its interface and func-
tionalities are based on the Melanie gel image analysis system (mentioned
in the previous section). It runs on the latest Windows TM operating sys-
tems and accepts data generated from the majority of mass spectrometers
such as those supplied by Bruker, Waters, and ABI-SCIEX. It also
supports the mzXML 16 and mzData 17 formats. It is worth noting that
the mzXML team (http://sashimi.sourceforge.net/) provides various
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