Progenesis SameSpots customer quotes
"We are very happy with Progenesis Samespots, it has changed our traditional approach to 2DE analysis, it is great."
Prof. Maria Cavaletto
Univ Piemonte Orientale, Italy
"I directly compared SameSpots to competitor's software with the same set of gels. SameSpots is considerably more user-friendly and straight-forward. Therefore, the analysis is 4-times faster compared to the competitor software.
Especially gel alignment is easier and more consistent; the transition view is a very efficient tool to monitor the alignment process. One big advantage of SameSpots is that significantly fewer landmarks have to be set by hand to align the gels. 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. Finally, I also found some more spots regulated than with the other software.
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
"I think it (SpotCheck) is a very convenient and user-friendly module, and definitely of a lot of use for multi-batch experiments run over time and between different users as well as across sites. It allows the gel runner to carry out a QC easily without having to export to a statistician and will and allow an experimenter to improve their up-front QC as well as assessing gel standards between clients and experimenters.
The end result showing the most variable spots is helpful for quickly narrowing down the cause of any fails. So as well as a QC checker it could also help in terms of speeding up or easing investigation of why things are problematic with your 2D gel protocol.
I like the interfaces and find it very clear to use - very smooth, no glitches and no 'operating problems' of any kind that I found. The explanatory lists and links are good too. In summary, I think this is useful, is something I would use and recommend to others, will save time for users doing in-house QC, help with contract-type arrangements especially, and does a good job, nice one!"
Dr David Jackson
Research Fellow in Gel Proteomics, England, UK
"...Before we introduced SameSpots in our lab, gel comparison and image analysis was very tedious and time consuming. SameSpots make this analysis fast and reliable avoiding “ever-lasting” analysis and improving the lab production. One of the main advantages of this software is that you don't need to spend a lot of time on training novices as this software is very intuitive and user-friendly. Before getting SameSpots, the main problem was to spend a lot of time in the image analysis. Since we have SameSpots we are more worried about the 2D gel quality than the further image analysis.
As you can perform the image analysis very fast, the publication rate is higher. Moreover, the comparison between gels performed by SameSpots is by far much better than others software packages (even the most expensive one!!!). Finally I want to thank Progenesis for doing a software that has been developed for scientists, not for software developers."
Institut de biotecnologia i Biomedicina, Spain
"It took us several weeks to analyze dozens of gels using the old software or other company’s product, but in the case of SameSpots, it is only several days. So, the great virtual of this software is its speed and automatics. We can get more time to do more research, also including training novices, writing papers. Among the new features in v4 compared with the old version, I pay more attention to the module which can help with the assessment and improvement of quality control. Because I think, to get more reliable result from the 2D data, it is especially important to evaluate the reliability of the data."
Jinshan Li on behalf of Dr Wei Wang
Hamburg University of Technology, Germany
"A few months ago, a "Samespots" demo session gave us the impression of an easy-to-use application. Now, we have finally bought the program... and our initial idea has been completely corroborated; very easy to use and very reliable results!"
Dr Marcel Koken
CNRS UMR6539 LEMAR, France
"I am using SameSpots to analyse my 2 D-DIGE gels. The software is really easy to use with minimum time for the analysis. I also appreciate the multivariate data analysis function in the software as well as the ease of exporting the data to other file formats for further analysis."
Dr Sanela Kurtovic
Atherosclerosis Research Unit, Karolinska Institute, Sweden
"Previously, we always considered 2D image alignment and analysis to be one of the big bottlenecks in 2D gel proteomics. SameSpots has completely changed that. 2D gel analysis is now easy and we do much more 2D experiments."
Jesper Hedberg, PhD
Molecular Toxicology, AstraZeneca RD, Sweden
"Since we started to use Progenesis SameSpots, all of our quantitative analyses are much easier, compared to when using our previous software."
URMITE UMR 6236, Faculté de médecine la Timone, Marseille, France.
"Progenesis SameSpots intuitive workflow makes 2-D analysis a relative doddle for students and infrequent researchers alike. The incorporation of FDR reporting (q-values) into the statistical analysis gives us much more confidence in our results."
Dr Dermot Morris
Teagasc, Animal Bioscience Centre, Ireland
"I am using SameSpots to analyse my 2 D gels based on silver staining. I am very satisfied with the software, since it has given huge improvements in analysis time and with good results."
Maria Louise Rentsch
National Institute of Aquatic Resources, Technical University of Denmark
"Progenesis SameSpots and Progenesis Stats has really taken our quantitative proteomics analysis to a higher level, for us, our external users and students in our courses. The workflow is now so much faster and reliable."
Dr Jorgen Bergstrom
Proteomics Core Facility, University of Gothenburg, Sweden
"We purchased the software Progenesis Samespots from Nonlinear Dynamics last year and the whole users is extremely satisfied with it. Indeed, its interface, even if in English, is very intuitive and each step of the electrophoresis images treatment is immediately comprehensive and easy to use."
Ecole Nationale Veterinaire de Nantes, France
"As a new user of Progenesis SameSpots, I felt amazed at how the use of the program is easy for spot matching and statistics. Several observations showed across different conditions a dose effect that occurred across the different treatments and therefore shows how this is a valuable program for 2D gel investigation and comparison. I did not see these changes with the other software packages I have tried."
Dr Vincent Blanckaert
Mer Molecules Sante, Universite du Maine, France
"I cannot believe the difference SameSpots has made to our discovery program! Differential analysis of our gels is now efficient and exciting rather than laborious and frustrating. I would not hesitate to encourage anyone who hasn't used the Nonlinear software before to try it as well as those who might have not looked at the package for a few years. We have greater confidence in our analysis and much better ways of looking at our results to aid in the proteomics process"
Dr Brad Walsh
Minomic Pty Ltd, Australia
"Progenesis SameSpots and its statistic tools have become indispensable in our gel based proteomics workflows."
Dr Friedrich Lottspeich
Max Planck Institute of Biochemistry, Protein Analysis, Martinsried, Germany
"Proteomics is a rapidly evolving multidisciplinary field of research. Recent advancements in mass spectrometry techniques set additional requirements on reproducibility, throughput, and thoroughness of quantitative proteomics for various applications. Effective and reproducible quantitative analysis is an essential and fundamental technique currently required by all proteomics laboratories. The Progenesis SameSpots software platform became the central platform for quantitative 2-D gel-based proteomic profiling performed in our lab."
Dr Alexander R. Ivanov
Harvard School of Public Health, Boston, USA
"Progenesis SameSpots is easy to use even for a novice. Our technician could apply it to our comparative studies after one day training. It is simple, quick and the stats behind are powerful. There is no need for perfectly reproducible replicates. The software tells you if the number of replicates is sufficient for your study. I can't believe I have spent so much energy on other software."
Sabrina Bousbata (Laugesen), Ph.D
Univeriste Libre de Bruxelles, Belgium
"Since more than 10 years, we used 2D gels to perform large and reproducible proteomic and immunoproteomic -or antigenic- maps. The complete analysis and superimposition of the gels with manual editing was time consuming and have inevitable bias. SameSpots has revolutionized this, producing objective, reproducible and swift comparison. Coupled to 2D-DIGE technology, this software is a real powerful tool in comparative proteomic, converting long days of "clicking on spots" to small minutes "automatically detecting spots"."
Laboratory of Immunopathology, Medicine School, Lille, France
"Progenesis 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, USA
"Since we have SameSpots, our proteomics studies have really improved. It is easy to use and allows you to quickly obtain good results with an high level of confidence."
Monzino Cardiologic Center, Milan, Italy
"I think SameSpots is one of the best tools I could imagine in the analysis of the 2D gels prepared after a huge amount of laborious work. All through the workflow - starting from the creation of the experiment to the statistics - the software has been designed to help the researcher.
Practical automated alignment (and choice of manual use) and data export as well as availability of utilizing a present project in order to analyze the data set according to a different grouping strategy are among numerous valuable properties and with each new version it transforms into a more user-friendly and time saving tool for 2D work."
Konak Med., Hacettepe Technopolis, Turkey
"We use 2D gels because they provide a reproducible and largely unbiased view of the proteome. SameSpots reinforces that objectivity and reproducibility, since it offers a superb automatic analysis combined with optimal reviewing tools. Hence manual editing becomes obsolete, saving time and -more importantly- avoiding the inevitable bias that editing introduces."
Novartis Institutes for BioMedical Research, Basel, Switzerland
"Unbiased differential quantitative analysis of clinical material can be performed by 2D-PAGE. However the high inter-individual variation usually found in clinical material demands for a method that allows for the analysis of large number of samples in combination with a small gel-to-gel variation. 2D-DIGE is a method that full fills the requirement for low gel-to-gel variation and a reasonable throughput. However, this approach only become useful if all protein spots from a large number of samples can be correctly matched in a efficient way. Progenesis SameSpots meet these criteria because it takes full advantage of the DIGE concept, not only for generating the quantitative data but also by its unique matching technology which generates a 100% match rate, regardless how many samples that are analyzed."
AstraZeneca R&D Molndal, Sweden
"Progenesis SameSpots provides an intuitive and comprehensive user-friendly interface that enables a rapid analysis of large 2-D gel data sets due to the reduced need for user intervention, such as spot editing and manual matching between gels. SameSpots enables us to apply objective statistical tests, and to visualise and organise meaningful results to achieve a clearer understanding of underlying relationships hidden in the data. We are finding SameSpots to be an invaluable tool in our Neuroproteomics and Cardiovascular Proteomics research programmes."
Professor of Biomedical Proteomics, UCD Conway Institute, Ireland and Vice-President of the British Society for Proteome Research, Dublin, Ireland
"We are really pleased we have chosen Progenesis SameSpots for our proteomics platform. We have already recommended it and will actively continue to do so."
Professor Catherine Guette
Laboratoire d'oncopharmacologie, Centre INSERM regional de Recherche sur le Cancer, Angers, France
"I would advise anyone performing 2-D analysis to give Progenesis SameSpots a trial, as I am sure you will be converted to this easy to use, hassle-free software."
Dr Ayesha De Souza
Cardiac and Vascular Sciences, St. George's University of London, England, UK
"Progenesis SameSpots and Progenesis Stats have simplified our proteomics research as the software is easy to use and the technical support from the Nonlinear Dynamics team is excellent."
Dr Roberta Pastorelli
Istituto di Ricerche Farmacologiche "Mario Negri", Milan, Italy
"To me the real breakthrough of SameSpots is that the analysis tools are no longer a limiting factor in obtaining reliable and reproducible results from 2D gels. Now the quality of an experiment is fully in the hands of the researcher: if this does not work, better go back to the lab and do a better job in designing the experiment and making the gels."
Novartis Institutes for BioMedical Research, Basel, Switzerland
"Progenesis 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.
The University of Texas Medical Branch (UTMB), USA
"The alignment procedure in SameSpots allows truly near complete matching of all spots across all the images of the experiment. And this is done in a fast, nearly automatic way. This makes not only image analysis much easier, and operator independent, but it makes statistics much more robust. Using SameSpots to analyze 2D-gel experiments, you feel much more confident that you are getting the most information out of the data. No worries about differences not detected as significant because of poor matching, ... without spending hours and hours reviewing the results. The built-in statistics provide also nice tools to check the consistency of the data through PCA analysis, find patterns of expression, and evaluate the significance of observed differences. By adding up simplicity of use and strong results, SameSpots has gone really close to what one would have dreamed of 2D image analysis software some years ago."
Institut de Recerca Hospital Univ. Vall d'Hebron, Barcelona, Spain
"Since we got the program a lot more people are doing 2D"
Dr Metodi Metodieb
University of Essex, England, UK
"Nonlinear Dynamics has identified the problematic issues associated with 2D analysis and solved them elegantly with SameSpots. 2D analysis is no longer a chore, more of a pleasure."
Dr Steven Banner
Neuropathogenesis Unit, Roslin Institute, UK
"SameSpots is the smart way for the 2D gel image analysis. No more subjectivity and iterative spot edition in the matching process. More importantly, the analysis is fast and straightforward thanks to the intelligent workflow, from image quality checking to gel alignment, to spot selection and edition and final results. In addition, the powerful statistic tools help to objectively decide in differential expression experiments."
Proteomics Facility, Universidad de Alicante, Spain
"The results obtained with Progenesis SameSpots are comparable to our current analysis package and took significantly less time to process. This has confirmed my view that SameSpots is superior to our current analysis package in terms of speed with the added advantage of a user friendly interface and statistical tools."
Dr Mark Weeks
Ludwig Institute for Cancer Research, UCL, London, England, UK
"Progenesis SameSpots is by far the best 2D gel quantification software I have ever used. It provides great improvement in speed and I like best its intuitive workflow. It brings my analyses to a new level of accuracy."
Dr Reto Portman
Friedrich Miescher Institut (FMI) for Biomedical Research, Switzerland
"We have enjoyed using SameSpots because it combines fast visual analysis, exceptionally reliable alignment and spot matching and quantitation as well. And it allows us to quickly focus the spots showing interesting expression patterns."
Dr Anna Chiarini
University of Verona, Italy
"We have a lot of experience analysing 2D Gels; we started using image analysis software in the mid-eighties. Since that time, we got almost everything available on the market. Progenesis is up to now the only software that gives us the full flexibility we need to analyse our gels. Now, I believe that by aligning the gels prior to the detection using TT900 S2S and then applying the SameSpots approach in Progenesis, I will be able to dramatically reduce my hands on time and further increase the level of confidence in my results."
Dr Delphine Vincent
INRA, Ferme du Moulon, Proteomics Platform, France (collaborator of Michel Zivy)
"Progenesis SameSpots represents a superlative software package to tackle 2D gel image analysis by means of an intuitive and unbiased workflow. The efficiency of gel warping and spot matching has greatly reduced the bottle necks in image pre-analysis processing. We have used SameSpots to analyse DIGE images of plasma and joint fluid from juvenile arthritis patients. The software allows us to quickly focus on those proteins which are sentinels of systemic or localised inflammation. With SameSpots we are able to highlight significant changes between patient subgroups with a higher degree of confidence, as previously overlooked missing values are now retained within the data set."
David S. Gibson
PhD Research Fellow Arthritis Research Group Queen's University Belfast Musculoskeletal Education and Research Unit, Belfast, N. Ireland, UK
"SameSpots is much advanced and ahead of its competitors. It has reduced the analysis time to minutes from hours. Its statistical power is unmatched; with the ability to find same spot on all of the gels on exactly same location, problem of missing values from the gels is gone. SameSpots is definitely better than previous versions and is much advanced than its competitors."
Ashutosh Gupta, student of Prof. Ramon Gonzalez
Rice University, Texas, USA
"By adopting these new image analysis technologies, our rate of discovery using 2D electrophoresis stands to be significantly enhanced. An additional benefit is that this new approach to 2D image analysis can be easily incorporated into our existing workflow"
Professor Steve Pennington
UCD Conway Institute, Ireland
"Everything about Nonlinear Dynamics makes it a great company to work with. The sales team really knows the product, technical support is excellent and readily available, and the software package itself is superb. The SameSpots upgrade gives an already great software package even greater accuracy. Being able to perfectly line up our gels increases the confidence we have in our results and reduces the chance for false negatives and positives. We would not do 2d gel analysis without it. The whole analysis process is easy, is highly accurate, and provides statistically meaningful results."
Merry L. Lindsey, Ph.D.
Assistant Professor, The University of Texas Health Science Center at San Antonio, USA
"The Mass Spectrometry and Proteomics Facility at Montana State University possess several 2D image analysis software packages. As an open access facility with user experience ranging from undergraduate to faculty level, we have been very pleased with the ease of use of the Progenesis SameSpots software. The image pre-alignment prior to spot detection is truly a step forward in analyzing gels with high batch-to-batch variability such as human depleted serum sample analyses. The intelligent noise correction algorithm and advanced background subtraction algorithms are important in spot evaluation. The inclusion of sophisticated statistical analyses products is a boon in the examination of disease-dependent alterations in human tissues/serum. We strongly feel that the Progenesis SameSpots algorithm is step above other commercially available products."
Dr Rachel Neal
Mass Spectrometry and Proteomics Facility, Montana State University, USA
"The differences between Progenesis SameSpots and traditional 2D analysis are profound. The old way required extensive spot editing and manually correcting the matching, which took a very long time. With SameSpots, the analysis is much less time-consuming."
Nancy Kendrick, Ph.D.
Kendrick Laboratories, Wisconsin, USA
"TT900 S2S incorporating SameSpots delivers an alternative starting point for 2D image analysis - offering significant improvements in image matching. The benefit of reliably matching spots across all gel images from the start means you can quickly focus your research efforts on investigating the few spots showing statistically valid changes, which are indicative of potentially interesting expression profiling changes"
Professor Mark S. Baker
CEO, Australian Proteome Analysis Facility Ltd (APAF), Australia
"Since implementing the SameSpots approach, the changes we have noted in our analysis have been very encouraging. The ability to perfectly align images within the experiment before applying SameSpots detection dramatically improves matching performance. This enables highly consistent and reliable results to be obtained from all our 2D data sets, even those that previous image analysis packages were unable to accurately quantify"
Dr Peter Ashton
University of York, England, UK
"SameSpots is a new way to think about 2D gel analysis. Now you can enhance the sense of your raw images for a more accurate and less time-consuming data mining."
"I am a fan of the new SameSpots approach which allows me to easily realign my gels prior to analysis. SameSpots also reduces my hands on time while increasing the quality and the level of confidence in the results produced. I am very excited to be pioneering this technology."
Dr Jean Louis Dacheux
INRA Nouzilly, France
"The SameSpots option is simply wonderful and I am so happy because it makes life so much easier for us! Currently we finalise several large 2D projects and spend so much time to find the significant alterations - which will be so much easier from now on. To give you an estimation spot correction based on detection and comparison to a reference gel took about 3-6 hours per gel. Now we only need to align the gel, which takes us about 30-45 min per gel."
Associate Professor of Medical Biochemistry, Medical University of Vienna, Austria
"The major advantage of the software Progenesis SameSpots is the ease of alignment of the gel images with conservation of the aligned images. We particularly appreciated the efficiency of the team of Nonlinear Dynamics during our first steps with the application."
Drs Catherine Grenot and Francoise Descotes
Centre Hospitalier Lyon Sud, Lyon, France
"I installed SameSpots and the only problem I have with it is that I am getting addicted to working with it! I don't think I could go back to working with any other software"
Forest Genetics, Technical University of Munich, Germany
"We used to spend a lot of time in matching gels after spots detection and SameSpots revolutionizes the usual strategy by starting to align gels before. The way they develop saves time and energy with an increase confidence in the results we get, by applying co-detection and noise removal."
Dr Christian Beauvallet
INRA, GPL/GEL, France
"Before SameSpots the time limiting step in our 2DE work was the image analysis now it is the production of 2D gels. The image alignment prior to spot detection and quantification performs really robust and reproducible. In a 2D data set the spot detection differs depending on which gel is chosen as reference, but due to the 100% matched data and no missing values the final results are very close to the same, independent of the chosen reference gel. This demonstrates a high degree of objectivity in the fast and nearly hands-free image analysis by SameSpots, increasing our confidence in the obtained results."
Dr Flemming Jessen
Danish Institute for Fisheries Research, Denmark
"We have used 2D analysis software from NLD since the very earliest released versions but with SameSpots we have significantly improved our approach to processing 2D gel data. We can compare 2D gels more efficiently with a high level of confidence in the derived data. The combination of the new warping routines and robust protocols for spot detection across the gel series means that we can now redefine our whole workflow in the use of 2D gels for proteomic research."
Phillip Cash PhD
Department of Medical Microbiology, University of Aberdeen, Scotland, UK
"SameSpots nous a apporte un gain de temps enorme dans le traitement de nos gels. Il est assez intuitif et nous sommes vraiment tres heureux de son acquisition. Le point le plus important pour nous est la fonction "100% matched data" qui assure a mon avis un meilleur traitement des resultats."
Centre de Lutte contre le Cancer Paul Papin de Angers Laboratoire d'Oncopharmacologie, France
"Performing alignment before spot detection reduces drastically the analysis time and improves the matching performance. Consequently, the quality of statistical data improves and any significant alterations can be easily calculated. By using completely matched experiments the impartiality of analysis is warranted, giving confidence in results collected."
Prof. Lello Zolla
Universita della Tuscia, Italy
"I am very happy with the software - I started with Phoretix 2D several years ago at Dartmouth College, and every time I use a new version I am impressed. It seems the programmers are really listening to what's needed by the users and are incorporating those features."
Dr Naomi Etheridge
University of Queensland, Australia
"Using SameSpots, I have managed to get more out of my data in the last week than I have done in the last 2 or 3 years"
Phillip Cash PhD
Department of Medical Microbiology, University of Aberdeen, Scotland, UK