SameSpots - 2-DE and 2D DIGE Analysis Software

Overcoming common challenges in 2-DE Proteomics research

SameSpots (previously Progenesis SameSpots) overcomes the common problems you face when using 2D gel electrophoresis to identify differential protein expression analysis such as lack of reproducibility in results, hours of tedious spot editing and a lack of 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 2-DE 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.

If any quality issues are detected with your images prior to analysis, you also have the opportunity within the system to make minor changes, without changing the original image. This includes flipping images horizontally and vertically, rotating images 90° clockwise or anticlockwise, inverting the image and cropping the image. To see how SameSpots can be used in your lab contact us for a free trial.

Our SameSpots software is trusted by the world’s leading educational, industrial and pharmaceutical companies

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We moved to SameSpots as it gives much more robust analysis of DIGE experiments - no ‘missing data’ issues and lots of statistical tools. The other major factor is that TotalLab is continually improving the software and works closely with customers to respond to their needs and suggestions.

Mike Dunn
- Professor of Biomedical Proteomics, UCD Conway Institute, Ireland and Vice-President of the British Society for Proteome Research, Dublin, Ireland

How intelligent automatic alignment leads to more accurate identification of spot patterns

We’re often asked if DIGE gels can be used within SameSpots and the answer is, ‘yes’. The DIGE experiments can be set up before alignment and the SameSpots software automatically deals with all measurement calculations.

We use alignment, which takes two images and overlays them in the same co-ordinate space, so that a spot on image A will be in the same location at the matching spot on image B.

Images can be accurately compared as alignment removes the positional variation between images, which may be introduced during the gel running and imaging processes. This allows for all images to be overlaid on each other and a single spot pattern to be detected. This image alignment delivers 100 per cent matching, with no missing values in your data, for valid multivariate statistics.

The software then uses intelligent automation to analyse results and produce automatically calculated dendrograms of spot relationships.

SameSpot automatic alignment screen
SameSpots Experiment Comparison

"SameSpots has greatly reduced the time needed for 2D-DIGE analysis. I can now complete an analysis in less than one-quarter of the time that it would have taken when using the previous supplier's software, while at the same time obtaining more consistent and reliable results due to the excellent gel alignment and spot matching features. SameSpots is also very easy to use and makes spot editing across gels as simple as just one click, rather than having to visit each gel individually to make all of the changes. I have no doubt that SameSpots will very quickly pay for itself in the terms of salary time alone."

Todd M. Umstead
- Pennsylvania State University College of Medicine

Delivering confidence in your 2D gel electrophoresis image analysis

The software is easy to use, with our experienced team providing you with a guided walkthrough of the workflow so you can quickly get to grips with the 2D gel electrophoresis image analysis software.

Once up and running, typical analysis takes just five minutes per gel with either single-stain or 2D DIGE images.

Quick tags can also be used: these are useful for quickly highlighting proteins that show significant changes in expression. Therefore, you can focus your attention on these ‘interesting’ spots for further analysis with mass spectrometry. You can also import protein identification from mass spectrometry, from databases such as MASCOT or your own custom-made databases, back into your 2-DE analysis and report alongside quantitative results.

3D SameSpots spot view
SameSpots 2D expression profile

SameSpots is user-friendly and straightforward. Therefore, the analysis is 4x 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

Case Studies

Case Study: University of Texas Medical Branch, Biomolecular Resource Facility

The University of Texas Medical Branch, Biomolecular Resource Facility is one of only seven sites within the USA that receive multi-million dollar state funding by the US Department of Health & Human Services.

Biomolecular Resource Facility NHLBI Proteomics Center

“The fundamental concept (image alignment) of SameSpots permits us greatly increased confidence in quantification, and this is enhanced when performed on gels obtained by our saturation fluorescence strategy. The statistical package further enhances confidence in our quantitative studies. In addition SameSpots has increased our throughput – with the demand we experience, this results in tremendous savings in manpower and expense over a year. With the proper tools and attention to detail proteomics can reap enormous benefits whatever your field of biological study. SameSpots is one of the tools that are indisputably required — providing the image and subsequent statistical analyses that are critical to a conclusive and compelling proteomics study.”

John E. Wiktorowicz, Ph.D. Associate Professor, Dept. Biochemistry & Molecular Biology Director, Proteomics Section

Case Study: Istituto di Ricerche Farmacologiche “Mario Negri”

Founded in 1963, The Istituto di Ricerche Farmacologiche “Mario Negri” is a non-profit independent scientific organisation for biomedical research and education. “In the Environmental Health Sciences Department we investigate the effect of environmental factors on human health, focussing on the survey of environmental contaminants, the assessment of human exposure with related health.

“We have been using SameSpots in our research since January 2007. The software has drastically simplified our proteomics workflow and opens up new avenues for the exploration of the data obtained”

“Since using SameSpots the speed of our analysis has been drastically improved. We align our gels accurately within 5 mins per gel and then run the SameSpots analysis. We don’t usually perform any correction of spot detection which results in fast, robust and very reproducible analysis. This has an immediate positive effect on the quality and confidence in our results.’’

Dr Roberta Pastorelli, Head, Protein and Gene Biomarkers Unit Laboratory of Molecular Toxicology

Case Study: Cardiovascular Sciences Research Centre, St. George’s University of London

The Cardiovascular Sciences Research Centre, St. George’s University of London, is a multidisciplinary group which amalgamates clinical, surgical and basic science research expertise. The mission of the Research Centre is to understand mechanisms of cardiovascular disease.

“The main difference is the speed at which we can analyze our gels. Using SameSpots, we are able to analyze our gels in a much shorter time frame, with very little manual intervention required. Initial analysis that could take days before can now be achieved within a few hours, obviously depending on the number of gels. The results we are obtaining are extremely robust and reproducible. The matching is excellent, and hardly any manual spot editing is required. Also, the inbuilt statistics is user friendly, giving both q values, which are extremely useful to have in addition to the p values, along with the power value. The workflow is straightforward and logical, and visually appealing.”

Dr. Ayesha De Souza, Senior Research Fellow, Cardiac Proteomics, Cardiac and Vascular Sciences, St. George’s University of London, London, UK.

Case Study: Centre Paul Papin

The Centre Paul Papin is a hospital specialized in cancer treatment and cancer research. The Centre Paul Papin collaborates with the Plateforme technologiqued’Angers which offers, among other things, services in proteomics to public laboratories and industry.

“With our previous software, we experienced three major problems. Firstly, despite the time we spent disposing of many landmarks on the master gel, the software made many mistakes in alignment. Secondly, when a spot was missing on the gel master, it was not detected and analysed. Finally, the software was not friendly to use and the analysis was laborious.”

“SameSpots is so convivial and intuitive that it is a real pleasure to work with. The image alignment step makes us feel secure that we have one hundred percent matching and the additional statistical tools are perfectly designed for biologists who are not specialized in statistics. The development and improvement of SameSpots has been pleasing.”

Prof Catherine Guette, Proteomics platform leader, Laboratoire d’oncopharmacologie, Nice, France

"For my Masters Class teaching at Lille University, I choose SameSpots as my favorite analysis software since it is easy to use, efficient, fast and intuitive. Its significant advantage is the statistical module! Last but not least, members of the Totallab company are very competent and reactive to solve any of my problems."

Estelle Goulas
- Université de Lille-Sciences et Technologies, France

How do we compare to the competition?

We’ve written a number of comparison guides comparing our software to the other 2D analysis products out in the market to show why we’re confident that we’re the best:

Why Upgrade from DeCyder to SameSpots?
Why Upgrade from PDQuest to SameSpots?

"We currently use SameSpots for our research projects and for training/teaching students on our MSc Genetics and Multiomics in Medicine programme. The software is extremely user-friendly and simple to navigate. The algorithm used for spot detection and spot matching across gels is fast and accurate. Very little manual editing is necessary, hence increasing the confidence of the statistical analysis without bias. The in-built statistical packages is straightforward to use and easy to interpret.

What sets SameSpot apart is the unparalleled support provided from the sales team of TotalLab. Dr Steven Dodd, Head of Sales and Business Development has always been there to provide continuous support to the students and myself in answering queries, concerns etc…”

Vaksha Patel
- Head of Genetics and Multiomics in Medicine Master's course, UCL, London


Our SameSpots software has been in active development since 2008 and in that time has been cited numerous times in proteomics publications within the field. It has also been rigorously compared to other pieces of 2-DE analysis software by independent parties:

Difference gel electrophoresis springer protocols journal of proteome research



“Although the image upload and project generation is comparable for DeCyderTM and SameSpotsTM, handling of the latter is more intuitive for the user due to fewer instances of user intervention (with respect to possibility and necessity) as well as its nonmodular structure allowing for a clear and coherent workflow, as reported previously [Silva et al., 2010]. Furthermore, markedly less time has to be invested for quantitative analysis since the warping technique combined with image alignment prior to coherent spot detection supersedes the time-consuming spot matching recommended in the case of DeCyderTM

Overall, even 40 years after the invention of 2DE and 20 years since 2D DIGE, the latter represents an affordable and valuable tool for high-resolution, quantitative differential proteomics. This is because of: (i) reduced costs of fluorescent dyes (due to meanwhile multiple vendors), (ii) time-saving and easy-to-use advanced CCD camera systems, as well as (iii) intuitive workflow and fast image analysis by warped, proteome map-based software, allowing for (iv) determination of highly similar, reproducible, and user-independent protein abundance changes.”

“In summary, SameSpots outperformed the other two software packages in matching accuracy, possibly being benefited by its new approach: that is, identical spot outline across all the gels. Interestingly, the statistical analysis of the software packages was not consistent on account of differences in workflow, algorithms, and default settings. Results obtained for protein fold changes were substantially different in each package, which indicates that in spite of using internal standards, quantification is software dependent. A future research goal must be to reduce or eliminate user-controlled settings, either by automatic sample-to-sample optimization by intelligent software, or by alternative parameter-free segmentation methods.”

You can find a comprehensive list of papers published using SameSpots here.

"I have been using SameSpots since 2014 in our both conventional 2-D gel analyses and DIGE Analyses. It allows us robust and user-friendly analyses, including gel alignment, spot picking and analysis, statistics, as well as reporting the results. Furthermore, the software has been improved since then, and we had never faced any struggles or difficulties using it."

Hasan Ufuk Celebioglu
- Associate Professor Department of Biotechnology, Bartin University, Bartin, Turkiye

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