Biomedical Engineering Reference
In-Depth Information
search engines cannot search the raw files directly; so they need
to be converted into peak lists first.
Producing a high-quality peak list from the raw data is cru-
cial to producing a high-quality protein database search result.
For best results, the peak list should be calibrated and deisotoped
with just the
12
C ions reported at the correct charge state. The
ideal peak list would contain the peptide fragment ions for the
MS/MS spectra and no noise peaks or extraneous masses but this
can be hard to achieve in practice and not always necessary as the
database search engines can cope with a fair amount of noise by
design. Some of the raw data-processing tools included with the
Trans-Proteomic Pipeline (TPP) can produce peak lists for raw
data as does the free toolkit ProteoWizard. A number of search
engines and LIMS include peak-picking tools and there is at least
one commercial program, Mascot Distiller (Matrix Science Ltd,
London, UK), that can open and process raw data files from most
instruments. The resulting peak list from all these tools is nor-
mally a text file formatted to match the input specifications of a
search engine. It is easy to convert these peak lists from one for-
mat to another.
A modern LC-MS/MS system can analyze tens of samples a
day, far too much to interpret manually. To efficiently analyze the
output of one or more instruments, a certain level of automation
is required. The raw data files are often processed through a soft-
automation features or a third-party automation client might be
used. The automation client is often included with the search
engine software; for example, Matrix Science's Mascot Daemon
is included with the Mascot Server software or the automation
scripts in the TPP. The data analysis pipelines may be built into a
Laboratory Information Management System that can automate
the data processing from acquisition to final reporting.
Table 4.2
Raw data-processing and format conversion software
http://tools.proteomecenter.org/wiki/index.php?
title
=
Formats:mzXML
http://proteowizard.sourceforge.net/
Mascot
Distiller
http://www.matrixscience.com/distiller.html
Spectrum Mill
http://www.home.agilent.com
Rosetta
Elucidator
http://www.rosettabio.com/products/elucidator
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