Progenesis SameSpots product overview

Progenesis SameSpots is the 2D image analysis product of choice if you use proteomics as a focus of your discovery research. Its unique analysis approach and simplified workflow deliver significant improvements in speed, objectivity and statistics. Progenesis SameSpots is also the only software proven to enable cross lab reproducibility.

Progenesis SameSpots v4.0 - unique analysis workflow

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. An image intensity histogram provides feedback on intensity levels in use and dynamic range of each image captured. 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.

Align Images

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, with 100% matching and no missing values, which radically reduces the need for editing spot detection and re-matching.

Control Detection Parameters - You have the option to select images that contribute to the generation of the SameSpots outline map – all of these images still have the final SameSpots outlines passed to them and are measured as part of the experiment. This puts you in control of the detection process and gives you the option to remove images from this part of the process should you wish.

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.

Filtering

This step allows you to remove artefacts from your analysis, based on normalised volume or spot area, and save you time at the review stage. You can also select areas of the gel to filter out, for example a damaged area, noisy area, spots on the edge of the gel or spots on the scanner bed.

Normalisation

You can visualise the results of normalisation on a scatter plot and the normalisation factor for each image. You can then take corrective action to ensure experimental quality is maintained. For added flexibility you can also opt not to use any normalisation in your experiment (non-DIGE only). For example in a dilution series experiment you would not want to use normalised volumes.

Experiment Design Setup

Set up experiment designs for all the comparisons you wish to make. You can choose to set up “between-subject” experiment designs and “within-subject” experiment designs (e.g. timecourse experiments).

Review Results - You can review statistically ordered lists of spots for all the experiment designs you set up using a range of displays. Spots are ranked 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. The streamlined workflow allows you to work logically through the spot rank table, accepting individual spots as you go or simply selecting the top ranked spots for further study.

In most cases you won't need to edit image analysis when you use Progenesis SameSpots, making it the most objective 2D analysis software available. However, if your images require some spot editing it only needs only to be performed on a single image with the effects applied across all the 2D images. This gives you a dramatically streamlined and simplified workflow.

Tags - This feature allows you to quickly create sub-sets of interesting spots within any groups being compared. The spots can be tagged based on meta-data, expression measurements or any user-defined criteria making them a highly flexible but simple way to display selected spot populations. Tagged spots can be analysed further in Progenesis Stats where they become even more powerful for surveying your data.

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.

Data import from external statistical analysis packages - When you import results which have been previously exported for further statistical analysis, it is now possible to label this data with a tag and link it back to the original spot data.

This means you can apply statistical tests using third party software that are 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 Progenesis SameSpots.

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.

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

Progenesis SameSpots v4.0 Feature Summary:

• Analyse single stain and 2D DIGE experiments. Supports .tiff, .img, .png, .gel, .mel images
• Use the alignment reference, spot outlines, notes and tags from an archived experiment
• Add images to any existing experiments or simply create new experiments
• Optimise analysis using initial automatic image quality assessment and feedback
• Perfect image alignment at the pixel level using a unique, simple visual application
• Select images that contribute to the generation of the SameSpots outline map
• Exclude artefacts, selected spots and any areas of your gel from the analysis
• Review the results of normalisation and take corrective action if required to maintain experiment quality
• Automatic analysis of the aligned image set and correction of dye related offsets in DIGE
• Choice of experiment design setups – either "between subject design" or "within subject design" with the option to set up multiple comparisons
• Automatically create a ranked list of significant spots based on ANOVA p-value for any experiment design set ups
• Review CV plot to check experimental variation is within the limits defined by your lab
• Perform editing on a single image for a dramatically simplified workflow
• Quickly create populations of spots with shared characteristics using tags
• Confirm hits using 2D and 3D montage views, expression profiles and spot data tables
• Easily apply multivariate statistical analysis on 100% matched data using Progenesis Stats
• Display interesting spots on a whole image view using Progenesis Stats
• Perform molecular weight and pI calibration
• Import results generated from an external statistical analysis package and link to spot data in Progenesis SameSpots
• Pick spots using a unique image alignment approach for high accuracy
• Supports most common spot cutting robots including GelPix, ProPic™ and Ettan™