Melanie Coverage Tutorial experiment

You can find the Coverage Tutorial files in the folder Tutorials in the software installation directory. They come from a 2D Differential In Blot Electrophoresis (2D-DIBE) experiment aimed at assessing coverage, i.e. the percentage of immunodetection that an antibody reagent offers for a population of HCPs. An E. Coli HCP sample was pre-labeled with Cy5TM and separated on a 2D gel. Protein was transferred from the gel to a membrane. The blot was then incubated with an anti-E. Coli HCP polyclonal antibody and […]

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Improve your productivity with keyboard shortcuts

Melanie has a few handy keyboard shortcuts to help you save time and effort. Select <Ctrl> + <A> Select all gels <Ctrl> + <Shift> + <A> Select all spots Undo/Redo <Ctrl> + <Z> Undo last action <Ctrl> + <Y> Redo last action Move/zoom <Left> Move left <Right> Move right <Up> Move up <Down> Move down <+> Zoom in <-> Zoom out <Ctrl> + <*> Fit images in screen <Ctrl> + </> Move images to same location Switch between stacked images <Page Down> […]

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Melanie DIGE Tutorial experiment

You can find the DIGE Tutorial files in the folder Tutorials in the software installation directory. They come from an experiment that aimed to study protein expression changes between control and treated groups of bacterial cultures. In this study, eight sample lysates were prepared; four were derived from treated bacterial cultures and four were derived from un-treated (control) bacterial cultures. Aliquots from each sample were taken and pooled to prepare a standard sample (pooled internal standard). The samples were run on four gels. […]

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Melanie Non-DIGE Tutorial experiment

You can find the Non-DIGE Tutorial files in the folder Tutorials in the software installation directory. They come from an experiment that aimed to study protein expression changes between four conditions. Cells were grown on two different substrates (Substrate A and Substrate B) and underwent one of two treatments (Treatment 1 and Treatment 2). Three biological replicates have been run for each condition (Gel1, Gel2, Gel3). Condition Treatment Substrate A_T1 Treatment 1 Substrate A A_T2 Treatment 2 Substrate A B_T1 Treatment 1 Substrate […]

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How does spot quantification work in MelanieTM?

In the detection step, spots are detected on a fusion image (which is not displayed, but which is generated based on the images marked for inclusion). The resulting spot pattern is propagated to the individual images, taking into account the deformation calculated in the alignment. For each spot on an image, MelanieTM  then computes the following quantification measures, based on the calibrated pixel gray values: Area: The area of a spot is the surface delimited by the spot border, and is […]

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The difference between a node-locked and a floating license

MelanieTM  supports both node-locked and floating (network) licenses. The following figure illustrates the two options. Node-locked license A node-locked license is locked to a specific computer. MelanieTM will only be able to run in fully functional mode on that computer. If you choose the node-locked license option: To obtain the purchased license, provide the Host ID of the computer on which you will run MelanieTM . Install MelanieTM  on the computer for which you provided the Host ID (with administrative privileges). Place […]

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How does normalization work in MelanieTM?

Why is normalization needed? 2D gel electrophoresis experiments typically aim at comparing different samples in order to identify protein expression changes that are characteristic of those samples. Nevertheless, relevant expression changes are often obscured by systematic experimental variation such as: Differences in sample preparation (inconsistent amounts of starting material, variations in reagents or protocols, pipetting errors) Differences in sample loading (pipetting errors, sample loss during gel loading) Differences in staining/labeling (inconsistent staining times, differences in labeling efficiency between CyDyes) Differences in image […]

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