We have collected here the most common questions regarding
Delta2D, its features, benefits and function. If you can't find
your question here, don't hesitate to
contact us.
1. What is Delta2D?
2. What advantage does Delta2D have over
traditional packages for 2D gel analysis?
3. What is Delta2D's approach to comparing 2D
electrophoresis gels?
4. What is the traditional approach to comparing
2D electrophoresis gels?
5. Besides comparison, what else can I do with
Delta2D?
6. What can I see in the evaluation version?
Delta2D is a new software for rapid visual comparison of 2D
electrophoresis gels.
From two gel images, Delta2D produces one dual channel image with
clearly highlighted differences in protein expression levels. The
dual channel image allows for the rapid visual identification of
whole sets of proteins whose expression varies from one sample to
the other or is influenced by an experimental condition.
Delta2D uses advanced image processing technology to compensate for
the variations in spot positions from one gel to another. These
variations make gel comparison a very tedious process, consuming a
large share of the time to analyze an experiment. The new
version 2.0 includes spot detection and quantitation.
The main advantage of Delta2D over established packages is speed.
Gel comparison with Delta2D typically takes only 20% of the time
that is needed with other packages. That means it saves 80% of your
time, time you can spend on doing something more productive than
"gel gazing".
For more advantages see the question "Besides comparison, what else
can I do with Delta2D?" below.
In a nutshell, Delta2D's approach to comparing two gels is:
- Load both images, they are automatically combined into
one false color image
- Mark a few pairs of corresponding spots
- Globally Warp one gel image such that the initial match
pairs are used for a global alignment
- Mark a some more pairs of corresponding spots to
compensate remaining distortions
- Exactly Warp one gel image such that the match pairs
are used for aligning the gel images exactly
- repeat steps 4 and 5 if there are any unaligned spots left
- Read the differences directly off the false color
image. Red spots are stronger on gel A, green spots are stronger
on gel B. Yellow spots have the same intensity on both gels.
Shades of these colors correspond to intermediate values.
- Quantify the spots using the segmentation tool, that is
available via the tools bar on the left or via the menu. Since
quantitation is based on advanced algorithms, you are asked to
define some parameters. In most cases the proposed parameters work
well and since the results are quite robust to parameter changes,
you should try them at first.
- Analyse spots and spot ratios studying the given table.
Sort or filter the table as needed and export the data of interest
in a common format.
This process is very quick because you have to assign only a
small fraction of the spots in order to get a perfectly aligned
image -- Delta2D's image processing technology does the rest. As a
result, you recognize those interesting spots earlier and more
accurately.
The
Delta2D tour demonstrates these steps in detail.
The traditional approach is:
This process is slow and tedious because of the necessary manual
corrections.
Fewer spot identifications: Warping gel images to a master
gel puts every protein spot to a "standard position". Thus when you
have identified a spot on the master gel you can identify it on each
of the other gels. This can save a lot of costly spot
identifications by mass spectrometry or protein sequencing.
Animations: When you have a series of gels taken at
different times you can warp them to one master gel before producing
an animation. There will be no "jumping" spots anymore so you can
concentrate on the changes in intensity over time.
Delta2D evaluation version is save-disabled but otherwise fully
functional. So you can see for yourself how it works and try it on
your own images.
