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.
Progenesis LC-MS customer quotes
"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 LC-MS 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 LC-MS 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 LC-MS 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 LC-MS has opened a new area in differential proteomics quantification, challenging isotopic labelling approaches ."
Dr Luc CAMOIN
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 LC-MS 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."
Dr Alex Jones
The Sainsbury Laboratory, Norwich, England, UK
"The advantage to us of Progenesis LC-MS 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 LC-MS 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
"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 LC-MS package has enabled our service lab customers to be taught in a very short time how to extract reliable results with 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
