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 easy, rapid and reliable analysis of 2D electrophoresis gels. It employs breakthrough image processing technologies that have been under continuous development since 2000, such as image warping for gel alignment and image fusion to create proteome maps. 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 aligning 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 Delta2D's approach leads to 100% spot matching, so that the time consuming manual editing of spot matching is obsolete.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 Proteome 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 HTML based web reports to see your analysis results.

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, or other applications like phospho staining, radiolabeling.

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

Of course, that depends on what software you are currently using Contact us for an in-depth answer.

Here is a partial list of Delta2D's main benefits - most of them based on Delta2D's unique features:

Reliable results thanks to a unique analysis approach

In Delta2D, you can take advantage of a unique approach (warping – fusion – spot detection – boundary transfer) that leads to 100% matching spots with quantitation on the original images only. Complete matching allows for applying advanced statistical methods, spot detection on one image — the fusion of all your images — saves a lot of time. Thus, you'll get more reliable in a minimum of time.

Intuitive user interface and workflow component

The recommended analysis approach for Delta2D is supported by a workflow component that leads you through the analysis. However, going back and forth is easy: You don't need to repeat each step you have already finished before.

Improved performance thanks to warping strategies and spot detection on one image only

Warping compensates for running differences between gels. With Delta2D's warping strategies you can organize the warping according to your experimental design: Create your own or select one of the pre-defined strategies. For instance, the Group Warping Strategy takes advantage of similarity of replicates. Thus, this strategy fastens automatic warping and simplifies manual quality control. Following Delta2D's recommend analysis approach, you create a fusion image for your project. The fusion contains all spots from all conditions. Thus, is a perfect image to detect a consensus spot pattern that can be used for all other images in the project.

Trust your results - apply advanced statistical methods easily

Delta2D offers many features (incl. views showing all images, customizable tables, dynamic expression profiles views, etc.) to check the quality of your results. Additionally, Delta2D incorporates the TIGR MeV tool which includes statistical methods such as t-Test, ANOVA, and non-paramatric tests like Wilcoxon or Kruskal-Wallis test to find differentially expressed spots. Many of these can be applied with false discovery rate (FDR) control. PCA, Hierarchical Clustering, and k-means/-medians clustering can be applied to find structures and identify outliers.

Exporting simplified

There are several options to export data from Delta2D. Besides basic features like image (e.g. as TIFF, PNG, etc.) and table exports (e.g. as csv file, to Excel, as pick lists), you are free to export data to Powerpoint (with spot boundaries and labels becoming real Powerpoint objects) or as interactive web reports in HTML file format.

Easily connect to web ressources

Our unique Scout technology not only supports data retrieval from databases such as UniProt and GenoList, the technology can also be used to connect your in-house databases to Delta2D. Data is appended to your labels saved along with your project.

Visualize results in your preferred way

Delta2D offers a wide range of features for visualization. They help you to get your data ready for publication and presentation. Among these are color coding for spots (e.g. according to their intensities under certain conditions) and color coding for labels (e.g. according to pI).

Premium Support is our Standard

With Delta2D you'll not only get an analysis software. Licenses include support: Our experts support you during your first steps with Delta2D... and even further.

All in one package and for all plattforms

If you decide for Delta2D, you don't need to purchase any additional modules, add-ons or something similiar. Delta2D allows you to analyze all kinds of 2D gel experiments such as classic stainings (e.g. Coomassie, Sypro Ruby, etc.), multiplexing (e.g. DIGE or Refraction-2D), phospho- or glycoproteomics, comparisons of 2D western blots with gels, and many more. Delta2D is based on Java. Therefore, you can use it on Windows, Mac or Linux based systems.

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) and another Refraction-2D, where multiple samples are labelled using different fluorescence stains and then comigrating on a single gel. For DIGE or Refraction-2D 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. If you entered valid contact data and information about your affiliation, you will receive a 30-days license file within two working days after download.

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, including devices made by GE Healthcare (formerly Fuji or Amersham), and Molecular Dynamics. Supported file formats include TIFF (8, 12, and 16 bit), JPG, JPEG, PNG, PNM, GIF, BMP as well as vendor-specific formats like IMG, or GEL. Please avoid formats that result in lss of information! 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.

Test the latest improvements in your own hands: The free evaluation version can be downloaded at http://www.decodon.com/Support/downloads.html.