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.

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

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?

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:

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.”

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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.