What are our customers saying?

Every so often one of our enthusiastic users emails us with some praise. It’s really appreciated and gives us an insight into how they are using Progenesis QI and Progenesis QI for proteomics. We thought we’d put some of these together in a way that answers the questions that scientists ask themselves when considering software options and share their experiences with you. We go through getting started to technical support. Please feel free to email us your own Progenesis feedback if you’d like to give us an endorsement for the website.

Progenesis QI logo Progenesis QI for proteomics logo

We are just starting label free, where do we begin?

“We are impressed by the user interfaces of all Nonlinear products, and Progenesis QI for proteomics is no exception. We have never done label-free quantitation before until we used Progenesis QI for proteomics for the first time. Some time ago, we did some shotgun proteomics on zebrafish plasma and thought we saw some interesting differences. We thought of doing label-free quantitation but were worried that we might need a long time to learn how to do it properly. To our surprise, with Progenesis QI for proteomics, we practically started getting publishable data within the first few hours. We started writing the paper while doing more experiments to confirm the quantitation. In 4 weeks, our paper was written! As usual, Nonlinear provided wonderful technical support for us. Label-free quantitation is now a routine technique in my lab.”
Dr. Lam Yun Wah
Department of Biology and Chemistry, City University of Hong Kong, Hong Kong

How do I analyze my large datasets?

“We have been running samples for 2 months non-stop, resulting in a data set of 1115 samples, each sample consisting of a 30 minutes gradient separation and an average of about at least 3000 compound ions per sample. A gradually increasing retention time shift up to more than one minute was observed towards the end of the gradient for the last 400 samples, but with Progenesis QI we could align all of them without any exception! This was a challenging task which to my opinion no other software would be able to handle!”
Geert Goeminne
Mass Spectrometry Expert, Department of Plant Systems Biology, VIB, Ghent University, Belgium

100% matching with no missing values Figure – Screenshot from the Progenesis Qi for proteomics software showing 100% matching with no missing values.

Am I detecting expression changes accurately?

“Progenesis QI for proteomics provided me an excellent tool to profile hundreds of proteins with incredible precision to map proteins in cellular compartments of the photoreceptor cells of retina.”
Nikolai Skiba, Assistant Professor
Albert Eye Research Institute, Duke University, USA

How do I avoid spending weeks analyzing my data?

“I am fascinated by the capabilities and efficiency of Progenesis QI for proteomics. One of the most important aspects of this software is the reliability of alignment algorithm. I had 36 LC-MS runs to align: the alignment score was > to 70% for all runs! It is very easy to use due to video tutorials and technical support. I analyzed all of my data in two days while it had taken up to one week on other software. Moreover, it is possible to tag interesting features and perform multivariate statistics based on ANOVA test which can be used in cases where there are more than two groups.
I tried many other software, but Progenesis QI for proteomics is the best I have used!”
Marianne Ibrahim, Ph.D
Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), Strasbourg, France

How can I reduce training time?

“The Progenesis QI for proteomics package has enabled our service lab customers to be taught in a very short time how to extract reliable results with which they are happy. The interface is truly intuitive and the alignment accurate and the results analysis package enables them to perform the work without the need for a statistician.”
Peter James
Prof. of Protein Technology, Lund University, Sweden

How can I analyze the data from all my different instruments?

“In my research of inflammatory diseases, I have successfully applied Progenesis QI for proteomics for the subsequent label-free analysis of our proteomics data from various samples ranging from highly complex tissue biopsies to semi-complex body fluids. The program supports an impressive range of vendors and search engines, and it is easy to import even complex experimental designs. Furthermore, the program is highly user friendly, allowing our students to use the program and analyze their proteomics data after only a short introduction.”
Tue Bennike
Laboratory for Medical Mass Spectrometry, Aalborg University, Denmark

How well is my software supported?

“Technical support for Progenesis QI for proteomics has been marvelous. Support personnel are knowledgeable, helpful and prompt. Given the complexity of some of the data that Progenesis handles, this level of support is vital.”
Kizhake V. Soman, Ph.D.
Assist. Professor of Biochemistry & Molecular Biology, UTMB NHLBI Proteomics Center, University of Texas Medical Branch at Galveston, USA

These are just a few of our favourites that we feel help in answering questions that new users and interested parties may ask when using the software. For more information and feedback on the software, you can also read other scientists’ reviews on our SelectScience pages for both the Progenesis QI and Progenesis QI for proteomics software packages.

If you would like to download the software and try it out on your own data, don’t hesitate to get in touch. We can get you started with the software. Isn’t it time you ANALYZED ALL of your data?