Updating from Progenesis SameSpots v3.0 to v4.5
Highlights of the new features you will receive:
pI and Molecular Weight Calibration
You can calibrate spots against either a molecular weight ladder or known proteins. Calibration values are added to the spot data table in View Results step.
Addition of second experiment design option
There is an option that allows the comparison of different samples from the same subjects, under different conditions. The software then performs a repeated measures Anova – the appropriate test for this type of experiment. You would use this experiment design for the analysis of a time-course experiment.
Import of protein identification data
Bring together 2D analysis results with MS-based protein identifications so you can put 2D results into biological context.
Quick Tags and Tag Filtering
The tags feature has been updated to improve flexibility and usability. Using the QuickTags feature, certain types of tag can be created without having to first select spots (for a specific fold change or Anova p-value). The tags filter dialog allows you to display spots on a selection of their tags so you can quickly reduce the amount of data you are viewing and concentrate on the spots of real interest.
SpotCheck is a separate QC workflow that allows you to quickly and objectively measure whether a 2D gel meets your lab’s quality requirements.
Find out more about the QC workflow.
Automatic reference gel selection
SameSpots automatically chooses which gel would make the best reference by doing a quick check to ascertain which gel image gives the best alignment results.
Unique ID given to spots
If you have more than one group set-up in your experiment design, you can change the comparisons being viewed and the spot ID is maintained. This means you can easily track a spot’s behaviour under different experimental group set-ups.
The clip gallery makes it easier to capture images and tables out of the software for the production of posters, publications and presentations. Images are saved as high resolution .png files (300 dpi) which are ideal for print.
Import of data from external statistical analysis packages
You can apply statistical tests using third party software that is specific for your research needs. The significant spots that you define can then be highlighted in an existing experiment and reported alongside the analysis results within SameSpots.
Visualisation of Normalisation
It had previously been very difficult to assess the quality of normalisation of measures in your experiment. This feature allows you to visualise the results of normalisation on a scatter plot and the normalisation factor for each image.
Visualisation of CVs
This is a useful measure to show spots with a high variance in measurement between gels. The CV plot helps you visualise the CV values and determine whether there is too much variance within the experimental condition so you can be confident your results are showing real changes.
Use alignment reference from an archived experiment
The spot outlines and any notes or tags from the archived experiment are copied to your new experiment. This gives the potential to copy protein identifications to the new experiment saving time and money on spot picking and mass spectrometry.
Improvements to Spot Picking
It is easier to align images with different resolutions, and their contrast settings are independent to help you visualise the images. This is especially useful when a separate picking gel is run and the image captured on a spot picking instrument. You can also zoom out of the spot pick point view and show it in whole image view to give you an additional visual check you are picking the correct spot.
Control over the SameSpots outline map
You have the option to select images which contribute to the SameSpots outline map putting you in control of the detection process.
Redesigned home page
See the latest blog posts and get links to relevant support materials from the redesigned home page. A search facility means you can quickly locate experiments in your list.