2D Gel Electrophoresis Analysis Software

Be confident in your 2D gel analysis results

SameSpots (previously Progenesis SameSpots) overcomes the common problems you face when using 2-D gel electrophoresis proteomics work to identify differential protein expression analysis. These include a lack of reproducibility in your results, hours of tedious spot editing and a lack of confidence in the resulting statistical significance of protein expression changes.

SameSpots is the complete solution for analysing 2-D gel electrophoresis and immunoblot images, it offers:

- - 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. Our next generation pixel-level image alignment algorithms deliver 100% matching with no missing values in your data for valid multivariate statistics.
  - 21 CFR or GMP-compliance. When combined with our AuditSafe software, allows users to meet and even exceed FDA 21 CFR part 11, EudraLex Annex 11, GAMP5 or more general GxP standards/ALCOA principles for compliance within regulated or QC environments, from captured image all the way through to final analysis and report production.

SameSpots is compatible with the latest version of Windows (currently Windows 11).

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

"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

Next-generation automated algorithms produce more accurate results, quicker

SameSpots uses a next-generation alignment-based approach to overcome positional variation introduced during the running and imaging of 2D gels which would typically prevent accurate comparison across multiple gels in large-scale proteomic experiments. These algorithms guarantee 100% matching of all spots with no missing values like those experienced in older pieces of 2D analysis software.

The software then uses intelligent automation to automatically detect all of your protein spots and copy a single spot pattern across all images which ensures a high degree of analytical objectivity and reproducibility as well as eliminating laborious spot editing typical to other pieces of spot-matching software.

Due to the automated workflow, the software is simple-to-use and easy-to-train on – typically taking less than 2 hours for a new user to become fully trained and ready to produce accurate results. Our advanced automation also means that the analysis of a full dataset of images (usually up to 24 images) typically takes less than an hour.

2D Gel Electrophoresis Automatic Alignment

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

Built-in Multivariate Statistical Analysis and Reporting Tools

Samespots is adaptable to your original experimental design, meaning you can perform full image and statistical analysis of your 2D proteomic studies within the same piece of software. This produces a comprehensive report that highlights to users when significant changes in protein expression are observed.

Samespots currently supports the following types of experimental design and associated statistical analysis:

• Between-subject Design (one-way ANOVA)

Do samples from your subject appear in only one condition (for example, only in a control group)?
Samples are grouped according to experimental condition (defined by the user) and an ANOVA test is performed to identify any significant changes in protein expression between those groups. The ANOVA calculation assumes that the conditions are independent and therefore gives a statistical test of whether the means of every single spot within all conditions is equal.

• Within-subject Design (repeated measures ANOVA)

Have you taken samples from a given subject under different conditions?
This specialist repeated ANOVA test allows the user to tell the software what experimental condition the sample came from along with the unique subject that the sample came from, ideal for longitudinal experiments where every subject has been sampled at every time point.

• Two-way ANOVA Design

Do your samples from a given subject appear in two different conditions?
The two-way ANOVA allows users to determine whether the effect of one of your independent variables (e.g. drug treatment A) on your dependent variable (e.g. protein expression) is the same for all values of your other independent variable (e.g. drug treatment B) and vice versa. This enables large scale clinical proteomic work to be performed between different drug treatment profiles and their effects on biomarker expression (significant or not).

Our software is regularly used in agricultural proteomics so the above studies can also be applied to testing variables such as genetically modified seeds, disease resistance, plant supplements etc.

"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

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.

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

Generate Picking Lists for Downstream Analysis

Once you’ve completed your analysis and identified proteins of interest within your experiment, what next? SameSpots fully supports d0wnstream protein identification via in-cell digestion and mass spectrometry via the export of industry standard picking lists.

SameSpots is also compatible with the majority of spot picking robots, exporting picking lists in their required file types to automate the process of protein retrieval from 2D SDS PAGE gels.

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.

“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 technologique d’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 several comparison guides comparing our software to the other 2DE Proteomic analysis software on the market to show why we’re confident we’re the best option for your lab:

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

Samespots vs DeCyder vs PDQuest

"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

Paul Dowling,
- National Institute for Cellular Biotechnology, Dublin City University

References

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

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.”

"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

Licensing, Solved

Here at TotalLab we’ve been working with pharmaceutical customers for decades and we know that some of our users prefer using air-gapped computers to enhance security within their sites. This isn’t a problem, all TotalLab software can be activated easily either online or offline.

Our licensing system licenses a whole computer at once, with no restrictions on the number of users who have access to the software on that computer.

Licenses can be purchased singularly for one computer or we also offer discounts on multiple license purchases at the same time if you want to cover multiple computers across your site; enabling hybrid working to perform analysis outside of the lab or to allow multiple analyses to happen at the same time.

We can also support enterprise licensing for full site-wide licenses covering large pharmaceutical manufacturing facilities and research facilities at a significant discount vs buying singular or multiple licenses.

For pricing and any other licensing related queries please contact us.

How to Purchase

The best way to ensure you’re purchasing the latest version of SameSpots with the highest level of technical support is directly from us here at TotalLab by using the contact us form. We can accept payment in GBP (£), USD ($) or EUR (€).

We do appreciate that some of our customers prefer sourcing products locally in a local currency or prefer to deal in their native language which may not be English. To facilitate this, TotalLab work with a global network of authorized distributors which you can find here.

FAQs

Can I account for spot distortions?

Yes.

Our unique, next-generation pixel level alignment algorithm makes it possible to accurately compare images by removing the positional variation introduced during the electrophoresis and imaging process. Making sure you only detect true changes in protein expression within your sample rather than from experimental or imaging variability.

Can I compare DIGE Images?

Yes.

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?

Yes.

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

Can I highlight proteins of interest?

Yes.

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?

Yes.

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

What Operating Systems can I use?

SameSpots is compatible with Windows vista, 7, 8,10 and 11.

What can I use to decide interesting spots?

There are many features to allow you to decide on interesting spots including:

Fold changes

P-values and Q-values

Correlation Analysis

Expression Profiles

Can I check my gel running quality?

Yes!

Our gel quality tool SpotCheck helps you objectively validate that your gel running meets your lab’s quality standards. It also highlights some common problems that occur during image capture.

Can I check my image quality?

When adding images to the experiment they are checked for quality and any issues/notes are highlighted for you immediately before any further analysis is attempted. Poor image quality can make analysis of your gels difficult. It can increase subjectivity and make your results less accurate.

What checks does Image QC do and what can I do to improve my images?

Image QC looks at and checks that images:

Are greyscale

Have a high bit-depth

Have a high dynamic range

Are free from saturation

Have not been compressed or edited prior to analysis

Can I edit my images?

Yes.

If your images require minor changes then you can edit them within the software without changing the original images. Edits include:

Flip images horizontally and vertically

Rotate images 90 degrees clockwise and anti-clockwise

Invert image

Crop image

How can I account for different gel loading?

This is accounted for by using normalisation. Normalisation is required in proteomics experiments to calibrate data between different sample runs. This corrects for systematic experimental variation when running samples (for example, differences in sample loading).

The effect of such systematic errors can be corrected by a unique gain factor for each sample – a scalar multiple that is applied to each feature abundance measurement.

What is Alignment and what problem does it solve?

Alignment 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 as the matching spot on image B. Alignment makes it possible to accurately compare images by removing any positional variation introduced during the gel running and imaging processes.

What is the Reference Gel?

One gel is selected to be the reference gel at the start of the experiment. This gel is used as the base for alignment so all other gels are aligned to this one. One gel is selected automatically but you can change this if you wish. An image with lots of clear, representative spots is best. The Reference Gel is only used for alignment.

How does Alignment work?

Can I calculate pI/MW?

Yes.

If one of the gels has a molecular weight marker on it and/or a pI strip or spots with known values then you can calculate the MW and pI for all spots

Can I import interesting mass spectrometry data?

Yes.

Results from Mass Spec, including MASCOT searches, can be imported into the program so you can look at and review this information in the program.

Resources

Image Capture Guide for Gel Electrophoresis Images

Good image capture is critical to guarantee optimal performance of automated image analysis packages and generate reliable scientific data. This technical document provides a brief guide to the range of different image acquisition devices currently in use for gel applications, defines some the important technical factors required to generate digital images of a quality suitable for automated image analysis and recommendations for producing good 2D gel images.

The Essential Guide to 2D Electrophoresis

Learn how 2D electrophoresis can separate proteins by isoelectric point and molecular weight, aiding in analysis and research. Perfect for understanding complex protein mixtures and identifying biomarkers.

How to Analyse 2D Gels

Discover the key steps of the SameSpots workflow and how it allows you to automatically analyse 2D gels with any type of staining including DIGE and DIBE.

2D DIGE vs 2D Gel Electrophoresis

In this short guide, we'll be explaining to you the technical process of performing 2D DIGE experiments and some of the advantages of using the technique over standard 2D electrophoresis.

2D DIGE vs LC-MS/MS

Dive into the world of precision and versatility as we explore the distinct advantages offered by 2D DIGE and LC-MS/MS for comprehensive proteomic profiling.

2D DIGE vs ELISA vs AAE for HCP Analysis

Explore the current landscape of anti-HCP antibody coverage with our article comparing 2D DIGE, ELISA, and AAE. Optimise your antibody selection process for robust anti-HCP analysis in biopharmaceutical research.

What are P-values, False Discovery Rate (FDR) and q-values in Proteomics?

In this article we explore p-values, q-values and false positives and give examples of how each are calculated within our 2D proteomics analysis software, SameSpots