Frequently Asked Questions

We have collected here the most common questions regarding Delta2D, its features and benefits. If you can't find your question here, don't hesitate to send us an email at info@decodon.com or contact us in another way.

1. What is Delta2D?
2. What advantages does Delta2D have over traditional packages for 2D gel analysis?
3. So, what does Delta2D do that I don't get with my present 2D gel analysis package?
4. Can I use Delta2D to analyze DIGE experiments?
5. Can I use Delta2D to analyze 1D gels?
6. I have downloaded the evaluation version. What's next?
7. What's different in the evaluation version?
8. What scanners and file formats are supported by Delta2D?
9. What automatic spot picking / spot cutting robots are supported?
10. I have downloaded and evaluated a previous version of Delta2D. What's new?

What is Delta2D?

Delta2D is a software for rapid and reliable analysis of 2D electrophoresis gels. It employs breakthrough image processing technologies that have been under continuous development since 2000. For more information about Delta2D please refer to the Delta2D product page. For an overview of what's new in the current version, see the release notes.

What advantages does Delta2D have over traditional packages for 2D gel analysis?

Delta2D is faster. With Delta2D, you'll only need a fraction of the time you spend with traditional packages. With SmartVectors Technology, Delta2D mimimizes the time needed for matching gel images to each other. Delta2D's approach leads to 100% spot matching, so that the time consuming manual editing of spot matching is obsolete. Spot detection and editing is only done for the fusion image, as opposed to each image. For a 24 gel experiment this means you only have to check and correct one set of spot boundaries, as opposed to 24 different sets.

Delta2D produces more reliable results. With Delta2D's 100% spot matching you get complete expression profiles for every protein. Besides higher throughput, this leads to significantly improved statistical confidence, so you can, for example, identify more biomarker candidates from the same experiment. Throughout the analysis, Delta2D gives you opportunities to do cross-checking, e.g. dual channel images to assess the warping, or direct display of the spot background image to assess quantitation.

Delta2D lets you do more with your data. For example, Delta2D's Protome Maps give you a high-level view on a whole experiment. You can make maps that contain all identified proteins, color code them to show protein properties such as isoelectric point and molecular weight, highlight proteins with specific expression patterns, and more. Getting data out of Delta2D is easy — use the convenient exports to Excel, PowerPoint, and Text (CSV), or use the raw analysis results in Delta2D's open XML format.

Delta2D is suitable for all types of 2D gel setups. You can analyze classical experiments as well as DIGE (Fluorescence 2D Difference Gel Electrophoresis) and other multiplex experiments using the same application.

So, what does Delta2D do that I don't get with my present 2D gel analysis package?

Of course, that depends on what your present software is. Contact us for an in-depth answer. Here is a partial list of Delta2D's features that are not available in most of the competing packages:

• An approach to spot matching based on image fusion and warping that eliminates matching problems. This is unique in Delta2D and one of the main reasons for higher productivity and reliability of results.
  
• Analysis of classical (single stain), DIGE and other multiplex experiments in one package.
  
• Great, fast qualitative image comparison based on whole image warping and dual channel images.
• Background subtraction based on whole image data. Unique in Delta2D.
• PowerPoint export where every label and spot is a real PowerPoint object that you can modify on the slide / poster.
• Image fusion for producing average images and proteome maps. Unique in Delta2D.
• Labels that do not get deleted when you edit a spot  (a problem in many other packages).
• Labels that can be transferred to / from a proteome map using the warping (packages without precision warping cannot do this).
• An approach to spot editing that is very reproducible. Delta2D uses minimal manual input, e.g. you click where you want to split a spot, as opposed to free-hand spot 'drawing', 'trimming', and 'erasing' in other packages. Unique in Delta2D.
• Compatibility with image formats (esp. calibration) of the whole Fuji FLA line, including the new FLA 5100
• Scouts that integrate protein information from web-based resources directly on the gel
  
• Spot color coding according to expression profiles (e.g. a proteome map where we compare three different conditions). Unique in Delta2D.
• Label color coding according to e.g. pI and Mw. Unique in Delta2D.
• Seamless integration with our proteomics information system Protecs
• Active development by a committed vendor with major upgrades every year.

Can I use Delta2D to analyze DIGE experiments?

Yes. Delta2D supports electrophoresis technologies that generate multiple images per gel. One of these is DIGE (Fluorescence 2D Difference Gel Electrophoresis), where multiple samples are labelled using different fluorescence stains and then comigrating on a single gel. For DIGE experiments, Delta2D supports all experimental setups, including those using an internal standard.

See Differential in gel electrophoresis (DIGE) - image analysis with Delta2D for more information.

Can I use Delta2D to analyze 1D gels?

It depends. Delta2D was developed and optimized for 2D gels. One-dimensional gels have different spot forms so you might have to use the spot editing more extensively. If the order of the lanes does not change between your gels, you can use Delta2D's warping to align different gels and produce expression profiles the way you would for 2D gels. In general, you'll probably be better served by a software package that is specifically developed for 1D gels, such as LabImage 1D.

I have downloaded the evaluation version. What's next?

Immediately after you have completed the download, you'll receive an automated email response with a license file that is valid for a few days. You'll need this file in order to be able to use the evaluation version.

For an introduction to Delta2D, please consult the Quick Guide from the Getting Started section in our documentation area. The guide will show you how to setup an analysis project and walk you through your first analysis session.

What's different in the evaluation version?

Delta2D evaluation version differs from the full version in two ways:

• It is not possible to save or export data produced by Delta2D in any way.
• Image files are overlaid with water-marks.

In any other respects, the two versions are identical, so you can see for yourself how it works and try it on your own images.

What scanners and file formats are supported by Delta2D?

Delta2D supports virtually all scanners in use today, incuding devices made by Fuji, GE Healthcare (formerly Amersham), and Molecular Dynamics. Supported file formats include TIFF (8, 12, and 16 bit), PNG, JPEG, BMP as well as vendor-specific formats like IMG, or GEL. See our Scanning Guide for more information about image file formats in general.

What automatic spot picking / spot cutting robots are supported?

Delta2D supports these devices:

• Genomic Solutions ProPic
• PerkinElmer ProXCISION
• Molecular Dynamics devices
• GE Healthcare Ettan Spot Handling Workstation
• Bruker Proteineer line
• Bio-Rad Exquest Spot Cutter
• Herolab Spot Hunter

Additionally, a generic format is offered which you can transform to control files for other devices. If a customer's device is not listed above, we'll usually create the necessary capabilities for free. The only condition for this is that the maker of the device makes available the specification of the devices pick list format.

I have downloaded and evaluated a previous version of Delta2D. What's new?

See the latest 'What's new in Delta2D' and release notes on our Delta2D Documentation page.