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Frequently Asked Questions
| Q: |
What is the difference between the two available versions of Melanie 7.0? |
| A: |
In addition to the features that are also present in the non-DIGE version, the DIGE version enables you to analyze DIGE experiments. It includes the powerful co-detection algorithm from GE Healthcare's Decyder software and a set of specific tools designed to optimally analyze DIGE experiments. |
| Q: |
What does "DIGE" mean? |
| A: |
Differential gel electrophoresis (DIGE) is a method for pre-labelling protein samples prior to two-dimensional electrophoresis. By allowing different samples to be run on a single gel, one of which can be an internal standard, it can significantly reduce the problems of inter-gel variations. The system is based upon the use of up to three cyanine dyes possessing unique flourescent properties. The dyes (Cy2, Cy3 and Cy5) are mass- and charge matched N-hydroxy succinimidyl ester derivatives that differentially attach to lysine residues in a protein. Therefore the labeled proteins migrate simultaneously on the 2-DE gel but still produce distinct excitation and emission spectra. |
| Q: |
Can I analyze images from 1-D electophoresis with Melanie? |
| A: |
Melanie has been designed exclusively for 2-DE image analysis. Its detection has not been optimized for the analysis of bands on 1-D gels, and therefore it is not recommended to use the software for 1-D applications. |
| Q: |
What are the image file formats supported by Melanie 7? |
| A: |
The supported file formats for gel images are MEL (Melanie/ImageMaster format), GEL (Molecular Dynamics), IMG (Fuji), GSC & 1SC (Bio-Rad), and TIFF (Tag Image File Format). |
| Q: |
Can I analyze gel images with white spots on a black background? |
| A: |
When you have such an image, you must use the "Invert Grey Levels" feature in Melanie to invert the grey levels prior to analysis. |
| Q: |
What should I do if the gels were scanned in different orientations? |
| A: |
It is really important that all your gel images are in the same orientationi. The typical orientation for a 2D gel is the following: - acidic end on the left and basic on the right.
- heavy mass on top and lighter on the bottom.
Melanie provides rotation and flip tools to easily correct a wrong orientation when needed. |
| Q: |
How many landmarks should I define on my gels before matching? |
| A: |
In most cases, very few landmarks are needed to match gels (between 0 and 2). We recommend to choose non-ambiguous, small and very well-focused spots. |
| Q: |
How do I find the most significant expression changes between classes of gels? |
| A: |
Melanie offers several possibilities to carry out statistical comparisons between populations of gels. You can find significant protein expression differences based on the probabilities from the ANOVA test, available in the Class Analysis Table. You can also use the Overlap values that are displayed in the Class Analysis Table. First, we recommend to filter the spots according to their Ratio (for instance, you can keep the spots that have a Ratio higher than 2), and then to sort the remaining spots according to their Gap values. Generally, this method gives very good results. Please note that this procedure is illustrated in the Quick Start Manual (QSM). |
| Q: |
Why are some menu options greyed out? |
| A: |
Menu options can be greyed out for different reasons. First of all, the DIGE functionalities are greyed out if your license is only valid for the standard package. Second, some operations can only be carried out if the appropriate objects (gels, spots, annotations, matches, etc.) are selected. Therefore, if a menu item is greyed out, make sure that the objects on which the operation should act are selected. Finally, depending on the context and especially the type of sheet you work in, certain operations can or cannot be carried out on the opened images (e.g. Detection and matching are not possible in the [ImagePool] sheet. Images must first be added to a project and opened in a [MatchSet] sheet to enable detection and matching). |
| Q: |
Where can I find the Host-ID of my computer? |
| A: |
In the case of the Melanie licensing system, the Host-ID is the Physical Address (also MAC address or Ethernet address) of your computer (NOT the IP address). To identify your Host-ID:- On the computer where the License file should be placed, select "Start > (All) Programs > Accessories > Command Prompt".
- When the DOS-prompt appears, click on it and enter the command "ipconfig /all" (making sure to leave a space between the ipconfig and the /all).
- Among the displayed information, make a note of the "Physical Address" but without and dashes or colons. If the computer has several physical addresses (there can be one for each network, i.e. Ethernet, card in the computer), any of them can be used for identification.
- Close the DOS-prompt window.
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| Q: |
How can I purchase Melanie 7? |
| A: |
Melanie can be obtained from GeneBio. To purchase the software, you can contact us here. |
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