How it works

The Progenesis SameSpots workflow allows you to analyse and compare 2D gels stained for protein expression as well as secondary stains, including:

• Phosphoproteins
• Glycoproteins
• Antibodies

Image QC

Your images go through a process of image quality assessment with feedback to help you optimise image capture - vital for accurate image analysis. Any positional errors introduced during scanning can be corrected using in-built tools (flip, rotate, invert) without interrupting your analysis workflow and images can be cropped if required before proceeding with the analysis.

Image alignment

You use this simple-to-use visual tool for highly advanced and automated image alignment. The result is perfectly aligned images at the pixel level, which enables 100% matching and no missing values after the automatic analysis.

Automatic Analysis

You can complete analysis of a whole experiment in this single step, which takes only minutes per gel. This incredibly rapid process includes SameSpots detection, background subtraction, normalisation and matching.

Review Results

SameSpots presents statistically ordered lists of spots for all the experiment designs you set up. Spots are ordered by p-value from the one way ANOVA analysis and given a unique ID which is maintained if the experiment design setup you are viewing is changed.

In most cases you won't need to edit the analysis, but if some spot editing is required, you edit on a single image and the effects are applied across all images in the experiment.

Statistical Analysis

Progenesis Stats is a simple-to-use tool that allows you to easily apply powerful statistical analysis and make reliable conclusions. Principal Components Analysis (PCA), Correlation Analysis, Power Analysis and q-values (false discovery rate adjusted p-values) are included to explore the trends in your data.

The tests enable you to measure:

• How your data clusters within your experiment. This can validate the hypothesis used to create the experimental groups and indicate any outliers in your data
• How similar spots are in terms of their expression profile. This can help you find additional drug targets or other proteins involved in processes related to the one you're studying
• The power of your experiment. This will tell you if you've run enough replicates for valid results and is becoming a requirement for publishing research

Any spots you select as being interesting from these tests can be mapped onto a whole gel image to show their location for further validation.

pI & Molecular Weight Calibration – The calibration feature allows you to quickly calibrate spots against either a molecular weight ladder or known proteins. The image can be tagged with MW and pI values and calculations are updated on the fly as marker points are added. You can view imported MS-based protein identification results and cross check against your markers to confirm their accuracy.

Spot Picking

The unique alignment allows you to align an analysed image to a picking gel and create highly accurate spot picking. The workflow supports manual picking, those using the GelPix, ProPic™ and Ettan™ spot cutting robots and there is also a generic robot option which outputs the spot picking coordinates.

Import Protein IDs

If you have identified proteins using Mascot, or have your search data as a .csv file, you can import results back into SameSpots linking identification data to the spot from which it originated. This gives you a complete view of your experiment and helps put results into biological context. Identifications are integrated into the SameSpots results tables and can be viewed on the whole image view.

Publish and Share Results

As you work through your analysis, images and tables can be added to the clip gallery with a simple right click. You also have the option to add some notes for future reference.

The report at the end of the workflow provides an overview of the protein spots you defined as significant or selected for picking. The printable report can be saved for future reference and is a quick way of sharing your results with colleagues.