Fast, easy-to-use and reproducible differential protein expression analysis


Why SameSpots?

SameSpots overcomes the common problems you face using 2D gel electrophoresis for protein analysis such as lack of reproducibility in results, hours of tedious spot editing and confidence in the statistical significance of measuring protein expression changes.

SameSpots is simple to use and gives you fast, objective results for differential expression of intact proteins using 2-DE gels.

  • Simplicity. You are guided through each step of the workflow, new users can get up and running with minimal training.
  • Speed. Typical analysis times of less than 5 minutes per gel with single-stain or 2D DIGE images.
  • Objectivity. A consistent analysis approach that is proven to give reproducible results between different users.
  • Statistical power. Image alignment delivers 100% matching with no missing values in your data for valid multivariate statistics.


Be confident in your 2-DE gel analysis results!

Check you can achieve reliable analysis of your precious samples early. SameSpots includes features to objectively measure the quality of your 2-DE gel running and scanning.

Quickly highlight proteins showing significant changes using our “quick tags”. SameSpots makes it easy to select interesting spots, pick them for mass-spectrometry, import protein identifications back into your 2-DE analysis and report alongside quantitative results.

Make it possible to analyse significant numbers of replicate samples within hours, not days, to control for biological and technical variation.

Achieve the quality of results journals demand for publications with valid multivariate statistical tests easily applied to your 2-DE analysis data.

SameSpots review of the same spots on all images. 100% matching.

SameSpots is considerably more user-friendly and straight-forward. Therefore, the analysis is 4-times faster compared to the competitor software. The minimal user intervention that is necessary to perform the analysis speeds up the process and ensures reproducibility of the results independent of the individual user. SameSpots will enable us to set up a rapid 2D gel analysis workflow to generate exact and highly reproducible data in our lab.

Dr Katja Schlink

Research Centre for Agriculture and Forestry, Laimburg, Italy

Book a demonstration of SameSpots


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Examples and evidence

Example SameSpots analysis report


This example report demonstrates how SameSpots was used to analyse a DIGE experiment. Spots of interest with a fold change greater than 2 and a p-value ≤  0.05 were highlighted between a treated and controlled condition in less than one hour. Read more…

Poster presented at HUPO: Healing the Achilles Hell of Proteomics - 2-DE Reproducibility Study

The SpotCheck feature of SameSpots was used in a multi-lab reproducibility study to measure gel running quality within labs and between labs. Poster was initially presented at HUPO conference 2010. Read more…

Technical Specification


SameSpots gives you the features you need to quickly and reliably analyse experiments:

Can I account for spot distortions?


Alignment makes it possible to accurately compare images by removing the positional variation introduced during the electrophoresis and imaging process.

Can I compare DIGE?


DIGE experiments can be set up before alignment and the software automatically deals with all measurement calculations.

Can I match all spots across all images?


Alignment removes positional variation between images, this is followed by co-detection of all spots on all images.

Can I highlight spots of interest?


Spots can be sorted by a range of criteria and the “tagging” feature allows spots of interest to be grouped together.

Can I export my results?


A HTML report can be created and all images can be exported using the clip gallery feature.

SameSpots is compatible with Windows vista, 7, 8 and 10. Performance depends on processing power.

Simple workflow


The simple workflow of SameSpots allows experiments to be analysed in hours not days!

Images: images are quality checked and any issues are flagged prior to starting the analysis. In DIGE analyses images are grouped by gel.

Alignment: Alignment removes the positional variation between images allowing all images to be overlaid on each other and a single spot pattern to be detected.


Automatic analysis: A single spot pattern is co-detected on all images in the analysis. P-values and fold change values are automatically calculated based upon the experimental design set up.


Statistics: Anova p-values, q-values, power analysis, principal component analysis and dendrograms of spot relationships are all automatically calculated within SameSpots.


Report: HTML reports can be automatically created at the end of the analysis. All images, graphs and tables can be exported using clip gallery and spot picking files can be created for manual picking or use with spot picking robots.



 Try SameSpots using our tutorials.

Try the simple workflow of SameSpots today using our downloadable DIGE and single stain tutorials and image sets.