Biology Reference
In-Depth Information
DIGE gels. Since the same proteins are localized in the same
x
- and
y
-coordinates on the gels, the spot detection procedure is the same for
the codetected gels. The matching step is thus straightforward and less
subject to error.
Free tools available through the Internet are an alternative to com-
mercial systems, although they are usually limited to simple operations
on a small number of gels. The free tool Flicker was created to visually
compare 2-DE gels.
9,10
It has a Java applet and a stand-alone version to
be installed on the user's computer. Both versions allow the visual com-
parison of two gels either side by side or superimposed. When gels are in
the overlay mode, “flickering” both images affects protein spot intensi-
ties so that expression is discernable. GelScape
11
is a Web-based tool to
display gel images and at the same time a database to house gels and their
annotations. The gels uploaded in GelScape can also be compared with
the other available gels in this database. The free Melanie Viewer has the
usual visualization operations of the full version and most of the analysis
procedures as well; however, the analysis is restricted to a small number
of proteins and only from gels that have already been analyzed by a full
version. The viewer version of PDQuest™ also gives the possibility of ele-
mentary visualization of gel images.
2.2. LC/MS Imaging for Label-Free Quantitation
An alternative, though common, proteomics workflow combines the sep-
aration of proteins and peptides by LC followed by direct analysis by MS.
This workflow has initiated the design of new bioinformatics tools for
proteomics that are complementary to 2-DE gel image analysis. In the
proteomics imaging of LC/MS studies, data are also represented in two
dimensions, i.e. the elution time and
m
/
z
, and they can be visualized and
analyzed as images. LC/MS image analysis, albeit being a recent pro-
teomics field (the first articles were only published in 2002
12,13
), shows
promising applications in differential proteome analysis by comparing
several label-free proteome sets and detecting significant quantitative dif-
ferences, and in discovering specific proteins. These expectations
certainly explain the sudden emergence of a number of packages within
a short period of time.
