Waters | Nonlinear Dynamics

Progenesis QI for proteomics

The next generation in LC-MS proteomics data analysis software.
Discover the significantly changing proteins in your samples.


Progenesis QI for proteomics customer quotes

“We are really impressed with how Progenesis increased our HCP analysis in terms of quality and throughput. By using spectral libraries and the new HCP quantification mode, Progenesis helps us to identify and quantify HCPs present only in trace amounts with high reliability. We can match identifications to signals over a high dynamic range, even if a high amount of drug substance is present. As a CRO, the aim of our customers is to ensure safe drugs – we can support them by giving them a reliable value of the HCPs present in their drug samples. Additionally, we are happy with the support Progenesis gives. The software is constantly in progress and Progenesis implements new features on request, wherever possible.”

Dr. Heiner Falkenberg
Team Leader Biotherapeutical Analytics, Protagen Protein Services GmbH, Dortmund, Germany

“In Dualsystems Biotech we specialize in elucidating protein-protein interactions at the cell membrane of living cells by applying the ligand-receptor capture LRC-TriCEPS™ technology. LRC-TriCEPS and the newest development HATRC-LRC are novel chemoproteomic approaches towards identifying cell surface receptors and off-targets of a ligand of interest. The methodologies include the following steps: ligand coupling to TriCEPS™ or HATRIC crosslinker, incubation of conjugate with living cells or tissue expressing target receptor(s), purification of crosslinked proteins, analysis by LC-MS/MS, label-free quantitation and statistical analysis to identify enriched proteins.

Progenesis QI for proteomics is our workhorse when it comes to data analysis. It is a user-friendly and intuitive software that does not require computational skills but still provides the user with time-efficient and powerful data analysis options, nice graphs and good scalability. What we enjoy the most while using Progenesis is the fact that there are no black boxes, the user has control over the data and can always assess the result of applied algorithms. This is particularly important during feature alignment where the user can visually inspect and also modify the alignment allowing for more robust quantitation and low percentage of missing values. A round of applause also goes to the team of technical support that are readily available and extremely helpful. We highly recommend using Progenesis QI for label-free quantitation and beyond.”

Dr. Paul Helbling, PhD
CEO, Dualsystems Biotech AG, Schlieren, Switzerland

“Progenesis QI, QIP and EZInfo package allows us to handle more proteomics and N-glycopeptide projects than ever in our career. Easy to use and easy to explain GUI enables efficient data handling and discussions with collaborators of various backgrounds easily. There is no difference if the project large or small, it is analysed in the same smooth efficient way, no matter if it is untargeted UDMSE or glycopeptide quantitation study. The integrated PCA-analysis is essential tool when sample set consists of different populations, phenotypes or unknown groups to visualize them in efficient way. NLD support is fast, efficient and always willing to work with you, which these days I find very remarkable.”

Sakari Joenväärä
Mass Spectrometry Expert/Laboratory Manager, Helsinki University and Helsinki University Central Hospital, Helsinki, Finland

“It's a pleasure to write a couple of sentences about “Progenesis QIp”. The main focus in our lab is targeted drug delivery research using nanocarriers, thus dealing with proteomes of human blood, as well as intestinal cells. The Waters' nanoLC-MS and Progenesis software help us a lot to untangle complex biological systems.

The Progenesis software has many advantages: easy to use thanks to its clear workflow; data obtained in a short period of time, powerful alignment; powerful statistical analysis; protein quantification; possibility to export the data easily, such as graphs, pics or protein measurements; FAQs; the software tutorials etc.

And last, but not least - the technical support team. Usually, we (the users) write to them for support. Here, it can also be the way around. From time to time, they write to you to check whether everything goes well. That's just great!”

Dr. Artur Ghazaryan
Max Planck Institute for Polymer Research, Mainz, Germany

“Progenesis QI is a valuable tool for us to carry out label-free differential proteomic studies. It presents a clear and intuitive workflow, making a easy to use tool of it. Its powerful data analysis capabilities have allowed us to deal with multiple experiments from different projects. The results obtained are robust, clear, and achievable in just a few hours. We have encouraged different colleagues to try it, because we really believe it makes a huge difference in label free differential expression analysis.”

Mikel Azkargorta, PhD
Proteomics Platform, CIC bioGUNE, Spain

“Since our lab is more and more involved in label free quantitation, Progenesis QI for proteomics has become a major part of the data analysis platform. Especially the “first quantify, then identify” approach is an enormous strength of this software. Moreover, the software is very intuitive and user-friendly, making your first steps in label free quantitation really comfortable. Doing label-free quantitation? Try this software out, and you’ll be hooked in no time!”

Paulien Meert, PhD student
Laboratory of Pharmaceutical Biotechnology, Ghent University, Belgium

"As a novice to label free quantification I have found Progenesis QI for proteomics to be easy, fast and effective. The tutorials are clear, the steps are easy to understand and technical support is readily available and helpful. A free trial period also is available which I highly recommend colleagues try with their own data."

Prof. Ross N. Nazar
Molecular and Cellular Biology, University of Guelph, Canada

"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

"The foundation of our data analysis software in the label-free relative quantitation of proteins is Progenesis QI. We especially like the alignment display, it has become an important QC parameter in our proteomics workflow. We find that statistically valid data pertaining to relative quantitation is dependent on the reproducibility of replicates for the peptide to be measured, and Progenesis does an excellent job at displaying this. Above all, it is user-friendly; anyone can pick it up and use it to look at relative changes in proteomes."

Dr. Ronan O'Cualain
Biological Mass Spectrometry Core Facility, University of Manchester, UK

"Over the past three years we have been facing increasing demand for label-free analysis on our proteomics platform. Progenesis QI for proteomics, with its user-friendly workflow, allows us to routinely propose relative quantitation to our customers.

As an example we were able to confidently identify biomarkers for DMD disease performing label-free analysis using Progenesis on a cohort of patients. Results were later confirmed with other techniques.

Progenesis QI for proteomics is powerful reliable software with a smart interface and statistical tools that provide robust results quickly."

Camille Garcia
Plateforme Protéomique/Spectrométrie de masse de l'Institut Jacques-Monod, Paris, France

"Another advantage of Progenesis QI for proteomics is the technical support team. My brute force, all-out frontal assault style of question-asking and attempts at “discussion” are always met with a quick and thorough response, it's been extremely helpful."

Paul Langlais
University of Arizona, Arizona, USA

"We like Progenesis because it allows us to separate quantification from identification which lets us build complex workflows, it is easy to use which is important in our academic lab, it is very sensitive to finding features of interest, the license system works very well such that we can install Progenesis on many PCs without restriction, and it is easy to use.

We have worked very well with the Progenesis team for more than 7 years and have great support in terms of prompt response to everything from simple questions to complex features requests."

Prof. Mark E. McComb
Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA

"We have been using the new version of Progenesis QI for proteomics to analyze a complex set of samples from an ambitious experiment. New users have got familiar with the application very quickly and have had the opportunity to try different protocols and experimental designs fairly easily. It is user friendly and allows to go back and forth through the workflow and to clearly visualize the results.

Moreover, the technical support is fast and has been very helpful every time we needed. The attention provided by the technical staff from Nonlinear was an added value of Progenesis from the beginning."

Prof. José Antonio Bárcena
University of Córdoba, Spain

"In just a short period of time, Progenesis QI for proteomics has become a key software tool in our data analysis platform. We use it for quick quality checks of our data as well as for complete, integrated label-free quantitative analyses. Its strengths include the accuracy of the alignment algorithm, the highly appreciated QC metrics section and the availability of the multivariate statistics tools. Moreover, it is very user-friendly and intuitive and the technical support is great. A must if you go for label-free!"

Elisabeth Govaert, PhD student
Laboratory of Pharmaceutical Biotechnology, Ghent University, Belgium

"I am quite satisfied with the recent implementation of absolute protein quantitation in Progenesis QI for proteomics 2.0. The Hi3-based method works like a charm, includes and deconvolutes all charge states and provides corrected quantification for homologous proteins and isoforms with shared peptides. Previously exclusive to PLGS/Waters, this combination of features is now uniquely platform-independent compared to any other commercial or freely available software, providing the most straightforward and accurate form of label-free estimation of absolute protein abundance to date."

Dr. Richard Sprenger
Department of Biochemistry and Molecular Biology
University of Southern Denmark, Odense, Denmark

"Progenesis was an easy-to-use and indispensable tool to define the content and quantity of subunits within samples and helped to define the search boundaries for other MS based approaches used in this study."

Dr Florian Stengel
ETH Zurich, Switzerland

"We use Progenesis for label free analysis of nanoLC-high resolution MS data, the software gives good opportunities for alignment, quantitative comparison and assigning identification to quantitative data. We were able to use Progenesis software for relative large numbers of samples (hundreds)."

Dr Theo Luider
Erasmus University, Netherlands

"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. In addition, the support from Nonlinear Dynamics revealed the gripping new features of the next version of Progenesis for proteomics at the 62nd ASMS conference (Baltimore, Maryland): the pathway analysis like IMPaLA and Panther, 'Hi-N' quantification and the best new feature 'QC metrics', so no more need to waste time to analyze our data manually! 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

"Gold standard for label-free LCMS data analysis across all instrument platforms."

Dr. Mark McComb
Boston University, Boston, Massachusetts, USA

"We went from spending countless hours analyzing thousands of lines on spreadsheets, to completely automated quantitative proteomics performed in only a few hours. We also significantly improved our MS approach, as a result of the excellent QC insight offered by Progenesis."

Paul Langlais
University of Arizona, Arizona, USA

"Progenesis QI for proteomics software is serving us well for label free quantitation. Its workflow is easy to understand and follow; that is making label free quantitation a preferred method for us. We would surely continue using this software and would also recommend to colleagues."

Dr. Vikas Kumar
Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences (NCBS-TIFR)
Bangalore, India

"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

"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

"The advantage to us of Progenesis QI for proteomics is the unbiased peptide-centric approach to quantitation. Significant MS1 peptides can be evaluated regardless of their identity status. The software is presented as a logical progression and the ability to analyse multiple sub-data sets within the one experiment, as well as tagging features makes Progenesis QI for proteomics an attractive tool that bridges discovery based research and candidate marker initiatives."

Dr Valerie Wasinger, Senior Research Scientist
Biomolecular Mass Spec. Facility (BMSF) at UNSW, Sydney, Australia

"I am very pleased with the Progenesis LC-MS Software platform. The video tutorials and technical support that are provided on the web site made it easy for my group to get started right away. We are in the process of integrating the Progenesis processed results into our label-free quantitative pipeline for all of our profiling studies. The peak detection browser is very useful, allowing us to review the processed data easily before sending FINAL results to our clients. The ability to make corrections from the aggregate view of the data and have it automatically pushed through ALL the LCMS files of the entire data set saves an enormous amount of time. We have observed that the FEATURE alignment is quite robust and reliable, showing that the processed accurate mass measurements and RT warping is implemented well. We look forward to using Progenesis to help us focus on those features that change significantly but were not MS/MS identified from the initial LC-MS/MS analysis. The feature-based quantitation will allow us to maximize the VALUE of the qualitative and quantitive information from all of our samples, particularly those where we only have limited amounts of material available."

Jeffrey C. Silva, Ph.D.
KinomeView & PTMScan Proteomics Service Manager, Cell Signaling Technology, Inc., USA

"The Progenesis proteomics and metabolomics products are intuitive and exciting pieces of software that allows rapid identification, quantification and interpretation of your data. The presentation of data and the options to highlight features allows the user to delve deeper into the mass spectrometry data with confidence and understand the results fully."

Dr G Don Jones and Janica Auluck
Department of Cancer Studies and Molecular Medicine, University of Leicester, UK

"Thanks to its accurate alignment algorithm, its statistical tools, its simplicity of use and the easy to understand data reports, Progenesis QI for proteomics has been fully integrated in our label-free proteomic workflows. Progenesis QI for proteomics supports data formats from all our different instruments and is also adapted to specific workflows such as gas phase fractionation that we regularly use.

Additionally, the very open and reactive support from Nonlinear Dynamics has been highly appreciated, as it has allowed us to interface rapidly and efficiently EasyProt (our platform for the analysis of MS/MS data), with Progenesis QI for proteomics."

Jean-Charles Sanchez and Alexandre Hainard
Proteomics Core Facility, Centre Medical Universitaire (CMU), Genève, Switzerland

"In addition to protein analysis, we have used Progenesis LC-MS in glycan LC-MS analysis to optimize our 'Label-free Differential Glycomics' platform. We have shown that Progenesis LC-MS is well suited to process glycan data also. In my experience, it is easy to use software with a straightforward workflow."

Jarkko Rabina
Research and Cell Therapy Services, Finnish Red Cross Blood Service, Finland

"This software from Nonlinear dynamics is the best I have used and it is undergoing continuous improvement. Everyone has their user preferences and no software can meet all expectations, but when issues arise the support is there, workarounds are created and user suggestions are taken on board.

We have, and continue to successfully use Progenesis LC-MS as part of our workflow for the identification of both biomarkers for neurodegenerative disease progression and moderators of neuronal vulnerability. This software has proven to be extremely useful when employed as part of a carefully considered experimental design."

Dr Tom Wishart
Molecular Neurobiology, Neurobiology Division, The Roslin Institute, Edinburgh University, UK

"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

"Progenesis is not only a great research tool but the tutorials are a great way to teach undergraduates through to researchers how to analyse and understand LC-MS data and analysis workflows."

Dr. Noel Carter
Department of Pharmacy, Health and Well-being, Sunderland University, UK

"Progenesis LC-MS is increasingly becoming a vital tool in high-throughput proteomics promoting numerous breakthroughs. Its user-friendly, simple and elegant approach allows even students such as myself to contribute highly in the scientific community."

Achilleas Livieratos
Department of Physiology, Anatomy and Genetics, Wolfson College, Oxford University, UK

"Progenesis LC-MS is successfully used in my lab not only to evaluate protein expression in solid sample, tissues and cells, but also in biological fluids by label-free approach. It is very easy to use and at the same time allows deep exploration of each determination. Students can use it after a very short training session. Results obtained with Progenesis LC-MS were found in good agreement with those obtained by Western Blot in a validation experiments. Moreover Progenesis LC-MS provides us with the differential expression of urinary and serum endogenous peptide."

Prof Fulvio Magni
Department of Health Sciences, University of Milano-Bicocca, Italy

"We have recently introduced Progenesis LC-MS in our lab and it has soon become the software of choice for the analysis of large cohorts of label-free datasets. The tool has major strengths in its intuitive GUI for data analysis and statistical interpretation. Its algorithms are very much appreciated, especially for the accuracy of alignment and peak detection. Customization of the normalization strategy and importing of identification results in standard formats make the software appealing also to the more picky scientists."

Bas van Breukelen and Salvatore Cappadona
Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University (a.k.a as hecklab www.hecklab.com), The Netherlands

"Progenesis QI for proteomics fits my vision of 'working smarter - not harder', offering a straightforward visual workflow and label free, absolute quantitation with the highest data completeness. The software has positively evolved over the years and keeps on improving with expanded features and increased automation, providing more insight while saving valuable time."

Dr. Richard Sprenger
Department of Biochemistry and Molecular Biology
University of Southern Denmark, Odense, Denmark

"We successfully analysed low molecular weight, low abundant peptides in a complex sample using a reliable fractionation process coupled with analysis by label-free nanoLC-MS. Progenesis LC-MS enabled us to analyse the label-free data from fractionated samples in a rigorous and reliable way and help us to generate a global view of the "peptidome" within mouse serum. Our platform, including this software, and our approach also show that by running simple checks you can minimise the fractions needed to achieve good peptidome coverage and so save instrument time and costs in achieving experimental goals."

Dr Geun-Cheol Gil and Dr Gabriela Chirica
Systems Biology Department, Sandia National Laboratories, Livermore, CA, USA

"Progenesis QI for proteomics software was introduced in our proteomics facility during the project of a master’s student. Despite student’s lack of experience in proteomics, the handling of the software was not a problem. The software was quickly evaluated thanks to a logical step by step intuitive presentation, user friendly interface and support from Nonlinear Dynamics.

Progenesis QI for proteomics has revolutionized our data analysis. In conjunction with high resolution LC-MS spectra, the software yields a complete comparison of a few dozen of LC-Run from complex samples in only a few hours. In our clinical analyses of biological fluids and tissues, we have to manage complex samples from individual patients. The label-free approach provided by Progenesis QI for proteomics yields a deeper proteome identification and quantification than isotopic labelling methods such as iTRAQ and SILAC. We obtain a higher number of identified and quantified proteins in less time and fractionation.

The multivariate statistics and the alignment algorithm are the cornerstones of the software. The power of the alignment algorithm allows perfect matching of LC-MS Runs. Statistical tools permit a relatively simple control of experimental integrity and help to focus on significant MS1 peptides. In conclusion, our purchase of Progenesis QI for proteomics has opened a new area in differential proteomics quantification, challenging isotopic labelling approaches."

Cancer Research Centre in Marseille (CRCM-UMR 891 Inserm), Institut Paoli Calmettes
Marseille Protéomique, France

"Progenesis LC-MS software and its statistic tools have become essential in our MS based proteomics workflows. For instance, one-dimensional LC separation, maximized by using a long gradient time in combination with long nano LC columns and coupled with high resolution/mass-accuracy MS results in a robust quantification of tens of thousands of isotope patterns. The possibility to perform multivariate statistics and tag interesting features is highly appreciated. In sum, label free MS-based approach using Progenesis LC-MS software overcomes many of the limitations of traditional proteomic methods leading to the comparison of protein expression profiles between multiple complex mixtures followed by a fast and effective identification of proteins of interest. In addition, the support from Nonlinear Dynamics is very responsive and each updates/patches of the software brings improvements."

Dr Aline Zimmer, Dr Maxime Le Mignon and Dr Julien Bouley
Stallergenes, Antony, France

"Progenesis QI for proteomics software has significantly improved our data analysis platform, as it allows us to do label-free quantitative proteomics acquired on instruments from various vendors. It offers the versatility to analyze complex protein samples separated at either the protein or peptide level and the statistical tools provided within the software give many options to test variation and ultimately get highly significant data."

Dr Leslie Hicks (Director) Dr Sophie Alvarez (Manager)
Proteomics & Mass Spectrometry Facility, Donald Danforth Plant Science Center, St. Louis, MO, USA

"Progenesis LC-MS provides us with rapid, easy to use, quantitative analysis. I could achieve more in a day using this program than I did in a week using other programs. The interface is so intuitive that the analysis of mass spectrometry data can come out of the support facility and back to the scientists, allowing one to focus on the scientific questions rather than being delayed by software issues."

Prof Alex Jones
School of Life Sciences, University of Warwick, England, UK

"We find the Progenesis software an interesting software tool to compare high resolution LC MS mass spectra obtained from complex samples such as cerebrospinal fluid, serum and tissue. We observe that relative large numbers of LC MS runs can be compared in a relative fast way. The results of Progenesis are of high standard. The assistance and the interaction with Nonlinear is highly appreciated. It leads to results that can be verified by independent technology."

Dr Theo Luider
Erasmus University, Netherlands

"We've introduced Progenesis LC-MS to our proteomics research for differential expression analysis of bacterial proteins, which can lead to improvements in biofuel production. Already it's proving very effective at visualising complex data; helping us to optimise the LC and MS conditions for optimal data analysis and generating reliable results."

Professor Gary Black & Andrew Porter (PhD student)
University of Northumbria at Newcastle, England, UK

"Progenesis LC-MS has allowed me to reliably detect and quantify the presence and absence of tryptic peptides and in different modified states as part of my research in determining Lyric ubiquitylation sites and monitoring changes in post-translational modification levels on single proteins. The alignment algorithms and ability to visualise LC-MS runs of complex protein digests have been invaluable in characterising this functional modulation."

Dr Karin Barnouin
London Research Institute, Cancer Research UK, London, England, UK

"Progenesis LC-MS has simplified the analysis of label free LC-MS data at the Institute of Functional Genomics Institute (IGF, Montpellier, France). The user friendly graphical interface provides an easy tool to check MS1 features detection and to present data to non specialists. The possibility to tag signals for targeted statistical studies and the possibility to build inclusion/exclusion lists for mass spectrometry makes Progenesis LC-MS a very versatile tool. The support from Nonlinear Dynamics has been very responsive and each new version of the software brings very welcome improvements."

Franck Vandermoere
Institute of Functional Genomics, Montpellier, France

"Progenesis LC-MS has simplified and enhanced the analysis of label free LC-MS data at the Conway Institute. An excellent feature of the software with respect to other available solutions is the alignment method which facilitates the generation of complete data matrices without missing values, making downstream analysis substantially easier. The package is very user friendly and intuitive enabling new operators at the Institute to effectively analyse data after just a few hours training with the tutorial that is provided. The inclusion of embedded statistics functions and simple data reporting and export make integrating label free LC-MS datasets into established workflows considerably more straightforward than has been previously possible. Additionally, the very high level of support from Nonlinear Dynamics has been most welcome."

Professor Steve Pennington
UCD Conway Institute, Ireland

"Progenesis LC-MS provides detailed control over the quality of the alignment. The integration of database search results for peptide identification into the quantitative dataset is very convenient including MSMS spectra annotation. Then, multivariate statistics has been made simple as a click. The ease of selecting and marking multiple (and overlapping) groups is great."

Dr Twan America, Group Leader Proteomics Facility
Wageningen University, Netherlands

"Progenesis LC-MS is amazing. You can interpret and assess your data easily, allowing rapid identification of interesting features in your results. Visualising data at the MS1 level is helping me to characterise a specific protein and uncover possible modifications."

Claire Jennings
University of Northumbria at Newcastle, England, UK

"The promise of high resolution XIC based relative quantitation has been severely limited for 2 years due to an inability to handle these complex datasets effectively. Progenesis LC-MS offers a user friendly interface with logical and simple progression through the data analysis process. Each quantitative observation is accompanied with fantastic levels of statistical analysis which facilitates an unprecedented level of data understanding with minimal user input. Moreover, Progenesis LC-MS allows rigorous global analysis of multiple datasets in an unbiased manner which is incredibly powerful when assessing the performance of your platforms over time. My recent purchase of Progenesis LC-MS has transformed label-free quantitation from an interesting academic sideline into a robust workflow that now challenges SILAC and iTRAQ workflows in quantitative proteome analyses in my laboratory."

Dr Duncan Smith, Head of Biological Mass Spectrometry
Paterson Institute for Cancer Research, University of Manchester, England, UK

"We recently integrated the Progenesis LC-MS software tool into our label-free protein quantification pipeline, since it is very easy to use, has a strong graphical user interface that allows straightforward evaluation of feature detection and alignment, and has powerful capabilities in statistical data analysis, a prerequisite for confident feature quantification. With the possibility to generate inclusion mass lists of significantly regulated features that can directly be imported into multiple MS-platforms, Progenesis LC-MS enables fast and comprehensive detection of protein abundance changes between multiple complex protein samples."

Dr Alexander Schmidt
ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland

"With the current move to non-gel based proteomics methods, we have been searching for a 'customer friendly' software that is both powerful, accurate and yet simple to use. Most of the non commercial software solutions, whilst sometimes excellent, mostly run from a very user unfriendly command line interface which is both hard to use and understand. 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

"We analyze surface structures, both proteins and glycans as well as their combinations, from various different cell types at Cell Surface Analytics Laboratory of Finnish Red Cross Blood Service. Here we utilize high mass accuracy mass spectrometer combined with nano-LC instrument. In these highly optimized and statistically designed experiments the data handling tends to form the most challenging and time consuming bottleneck. Lately, we have implemented Progenesis LC-MS as an integral part of our cell surface analytics workflows. Progenesis LC-MS enables label-free relative quantitation with speed and accuracy that matches our needs very well. The statistical modules of the software are often adequate enough to fulfil our experimental requirements. One of the most important aspects of the software in our hands is the possibility to perform quantitative analyses both on peptides and glycans. Although the Progenesis LC-MS has been developed for peptides, we have been able to utilize the Progenesis generated features for glycan identification with our in house developed software. In addition to excellent performance of the Progenesis LC-MS software, the customer friendly attitude of Nonlinear Dynamics is highly appreciated."

Leena Valmu, PhD
Adjunct Professor, R&D Manager, Finnish Red Cross Blood Service, Helsinki, Finland

"...The newer Progenesis LC-MS software seems to be a very powerful platform to assess quantitative characterization of complex proteomes at higher sensitivity using tandem LC-MS data and to advance the field of differential proteomics substantially. The effective and elegant statistical algorithms for peak alignment, data normalization and assessment of statistically significant changes in protein and peptide abundance between proteomic samples as well as impressive user-friendly visualization tools make the Progenesis LC-MS software a desirable platform for interpreting underlying molecular mechanisms of complex biological processes."

Dr Alexander R. Ivanov
Harvard School of Public Health, Boston, USA

"Progenesis SameSpots and its statistic tools have become indispensable in our gel based proteomics workflows. Recently we decided to use also Progenesis LC-MS in combination with the ICPLQuant software for the analysis of quantitative proteomics experiments using the multiplexed isotopic coded protein labeling (ICPL) method in combination with ESI-MS. The intuitive and unbiased workflow of Progenesis LC-MS makes the labor-intense data evaluation much more efficient. The support of the mz-XML data format enables the analysis of datasets acquired on many different MS instruments, eliminating the dependency on specialized vendors' software."

Dr Friedrich Lottspeich
Max Planck Institute of Biochemistry, Protein Analysis, Martinsried, Germany

"In our research and in the day-to-day business of a Core Facility Proteomics we are dealing more and more with quantitative proteomic approaches. With latest mass spectrometers and their high mass accuracy and good reproducibility of nano-HPLC separations as a essential prerequisite label-free quantitative analysis with Progenesis LC-MS and Progenesis Stats give us reliable quantitative data of literally tens of thousands of peptides in a complex mixture. Generating inclusion lists of interesting peptides with certain quantitative features but no protein ID for a second LC-MS/MS run is of huge benefit to the results of our projects."

Dr Hakan Sarioglu
Helmholtz Centre Munich, Germany