Status:
ReviewerMember since: 2019
Organization: SciMar Ltd
Useful for comparing LC-MS runs and identifying differences between them.
Application Area: Analyze small protein biomarkers in plasma
"The program is quite easy to use and has good tutorials. We received some training from a Waters application specialist that was very useful. We looked at other programs and chose Progenesis because of the cost to capability ratio."
Status:
ReviewerMember since: 2018
Organization: European Commission - DG JRC
Speeds up our workflow and fairly easy to pick up for new users.
Application Area:Analysis of food allergens in complex and processed matrices
"There is a great variety of possibilities in treating the complex mass spec data which makes it at first rather overwhelming to use. However, after having used a short while it is quite straight forward to use and has helped us simplifying complex data."
Status:
ReviewerMember since: 2019
Organization: Danone Nutricia Research
Good product but needs some work, price is one the high side, great alfter sales care.
Application Area:Proteomics, peptidomics, glycomics
"The product is user friendly but is missing some features for use with peptidomics, software is great for proteomics. Would also be nice to disable the auto save function, so you can go back to previous results. After sale service is good, timely response and good information. Product is high in price and missing some features that I would like to see. Also because there are two products that would be needed if you do small and large molecules."
Status:
ReviewerMember since: 2019
Organization: Fondation Méditerranée Infection
Powerful.
Application Area:Metabolites
"Easy to use and powerful software. It enables the processing of many raw files together and offers some useful statistics in order to extract interesting markers. It also enables the full processing of ion mobility data."
Status:
ReviewerMember since: 2018
Organization: Aarhus University
I am very happy about the results and I believe it is one of the best in the market.
Application Area:Differential proteomics
"Progenesis QI for Proteomics offers a ready to go workflow with sequential steps where intuitive options can be selected. The raw data if not centroids, is converted to accurate mass before being processed for alignment and further steps involve the MS1 peak peaking. After peak peaking a search engine will be chosen by the user according to the data/hardware of the MS instrument and assignment to peptides will be carried out accordingly to the post translational modifications selected. Optionally the user could export the peak list and import the searched ones by third part search engines. The statistical analysis is robust and protein and peptide review is easy to be achieved before final export of the data for further analysis. The effectiveness of the software over several competitors is worth money for the quality and the level of accuracy of the results/service that facilitate manuscript publication. Results are highly reproducible and accurate as well as it being possible to do label free absolute quantification by spiking a known protein hydrolysate to your mixture to be analysed."
Status:
ReviewerMember since: 2019
Organization: TMU
Can’t live without it.
Application Area:Analyze metabolites in clinical samples
"Easy to use. Helps users save a lot of time. I really like the function that generates reports in QIp."
Status:
ReviewerMember since: 2018
Organization: Bangor University
Excellent workflow for dealing with complex discovery data.
Application Area:Analysis of metabolites in plants
"Excellent workflow for dealing with complex discovery data from our Synapt G2-Si and or Q Exactive Plus. Can be configured easily for the needs of the individual user and is also great for making local databases with additional compound properties using Progenesis Metascope."
Status:
ReviewerMember since: 2018
Organization: University of Rijeka, Department of biotechnology
Great data analysis tool for label-free proteomics
Application Area:shotgun proteomics, label-free
"Easy to use (step by step approach), excellent tutorial and support, nice visualization of data"
Status:
ReviewerMember since: 2013
Organization: Iuliu Hatieganu University of Medicine and Pharmacy Cluj Napoca
Great results.
Application Area:Shotgun label free proteomics
"Very useful tool for comparative evaluation of proteomic data."
Status:
ReviewerMember since: 2018
Organization: King Adbullah University of Science and Technology
A good tool to use for Label-Free quantitation.
Application Area:Proteomics comparison in cells/tissue
"Prognosis QI is easy to use, quite intuitive, once you complete a section you input section complete and continue with the following. You can always come back and re-analyze the data. You can always contact the providers for any enquiry and get help from them. I consider it a worthwhile purchase."
Status:
ReviewerMember since: 2018
Organization: Functional Genomics Center Zurich
Good product for newbie user.
Application Area:Analysis and quantification of proteins in many samples
"The ProgenesisQI for Proteomics software is an easy to use software solution for quantitiative proteomics. Yet, it lacks a bit behind with what is cutting-edge in the field."
Status:
ReviewerMember since: 2018
Organization: University of Helsinki
Lovely piece of analytical software.
Application Area:Proteomics
"Results are consistent and software us powerful. updates useful for the user, so software is developing to the way users want."
Status:
ReviewerMember since: 2015
Organization: Ghent University
Progenesis QIP allows us to catch a glimpse of peptide emergence in proteomics
Application Area:Proteomics, histone epigenetics
"Progenesis QIP has facilitated our workflow in so many ways, it is hard to summarize. That is why I did a webinar on how it changed our data analysis workflow (http://blog.nonlinear.com/2018/03/28/proteomics-peptides-emergence/). In summary: In philosophy, systems theory, science, and art, emergence is a phenomenon whereby larger entities arise through interactions among smaller or simpler entities such that the larger entities exhibit properties the smaller/simpler entities do not exhibit. The most obvious example of emergence is life itself. Think about it: while anyone, or any algorithm, would still recognize you on a picture of 10 years ago (ok, not that one picture maybe), only a few molecules in your body are still the same as on that picture. It is as if you are the shape and matter is merely circulating through you, through time. Thus, explaining life itself by only focusing on the molecules we are built from and the laws of chemistry alone will be a dashing exploit. Yet, in proteomics, we currently have no other choice than to weigh molecular masses to fathom life. We need to be aware of this limitation and leverage knowledge with our mind, which actually is an emergent phenomenon in itself! If I have learned anything from the dozens of collaborations at our lab, it is that the term “Proteomics” is actually very confusing to the outside world. We measure peptides. What we actually report on, the proteins is merely inferred. In a time where productivity is key, people tend to focus only on trying to automate this inference. Yet, to date, only human intervention, i.e. the human mind, can assure that the most correct or least ambiguous outcome is reported. I would argue that proteomics is in itself an emergent – not “emerging” – field. Once you start to look at it like that, facilitating human inspection of the visualized data should be the primary focus in order to fill the gap between what is measured and what can be concluded in terms of potential biomarkers or biology. To illustrate this point, we look at histones in this webinar. These proteins are often used to normalize entire proteomes because they are rightfully considered as one of the most robust household genes in Eukaryotes. However, while these five low molecular weight proteins (10-25kD) have a very predictable expression profile, people tend to forget that they can get modified in ways that little other proteins can. Histones can theoretically generate roughly 7.1017 different proteoforms when you consider all the histone posttranslational modifications (hPTM) that have been previously reported. This translates into 50.106different peptide forms with ArgC-like specificity. Indeed, we do not measure the proteoforms in bottom-up proteomics and we do not consider each of these hPTM in the searches we do. This, in turn, implies that it is practically impossible to quantify these proteins accurately when you apply bottom-up proteomics. The fact that studying histone modifications is an intrinsically peptide-centric approach, however, made us realize that inferring protein abundance is extremely hard and in some cases even impossible. In this webinar, we will follow one such peptide on its journey through the Progenesis QI for proteomics workflow, to emergence. Using peak reviewing, QC metrics, conflict resolving and spectral library matching, we will detect artifacts, verify experimental reproducibility, detect outlier samples,… For histones specifically, it is invaluable that we can do several sequential searches (each with another combination of hPTM and using different search engines) and combine them all into this single analysis. Equally essential, we curate ambiguity that arises through these sequential searches by applying in-house scripting to the result files and then generate lists of tags to re-import into Progenesis QIP for manual validation and resolving conflicts. Because isobaric peptides carrying the same hPTM combinations elute very closely, we also manually verify and adjust peak picking of histone peptides. Finally, we are fascinated by the power of ion mobility separation in HDMSE acquisition and webinar concludes with a daring effort to match DDA libraries to HDMSE data. In conclusion, while this webinar follows very specific peptides, i.e. those derived from complexly modified histones, it mainly illustrates that no automation process to date is able to anticipate the complexity of protein abundance. I thus argue that the final list of e.g. potential biomarkers should always be manually inspected and visualized in order to save time and money in the downstream validation process. Indeed, Progenesis QIP allows us to peek behind the curtain and catch a glimpse of emergence."
Status:
ReviewerMember since: 2018
Organization: Medicago
Great results, fast process.
Application Area:Proteomics, analysis of impurities
"The service with nonlinear is always useful and fast. The new version of the software is a great improvement. Being able to see what peptide are used for the quantification is really helpful and helps get good results faster."
Status:
ReviewerMember since: 2018
Organization: Centro Cardiologico Monzino IRCCS
Good and fast results.
Application Area:Proteomic analysis of clinical samples
"We have been using Progenesis QI for proteomics to compare complex sets of samples analyzed with a label free MSE approach with different experimental designs. I can confirm that this is really powerful software, easy to use, with a smart interface and statistical tools that allowed us to speed up our analysis obtaining high confidence results."
Status:
ReviewerMember since: 2015
Organization: University of Maryland, School of Pharmacy
Progenesis QI for proteomics is an efficient and robust platform for proteomic data analysis.
Application Area:Biomedical research
"Progenesis QI for proteomics is an efficient and robust platform for proteomic data analysis. The workflow incorporates chromatography, ion-mobility, and data-independent high resolution mass spec acquisition. The platform is readily accessible and accommodates various data formats."
Status:
ReviewerMember since: 2014
Organization: Mayo Clinic in Arizona
Progenesis QI is a no-brainer for label-free quantitative proteomics.
Application Area:Quantitative Proteomics
"Progenesis QI has made our label-free quantitative proteomics extremely streamlined. In addition, Progenesis QI has been invaluable for troubleshooting and quality control. Progenesis QI is Proteomics 2.0."
Status:
ReviewerMember since: 2016
Organization: University of Leicester
Very flexible bit of software form biomarker discovery
Application Area:Biomarker discovery
"Progenesis QI is a smart intuitive way to analyze large data sets for proteomic and metabolomic studies. We have been able to translate many studies from discovery to verification or mechanistic studies using Progenesis QI."
Status:
ReviewerMember since: 2015
Organization: Tun Abdul Razak Research Centrel
Application Area:Protein expression changes in rubber root samples
"Because of our pleasant experience with Progenesis Samespot, we opted for Progenesis QI, we are not disappointed. We are routinely analysing root protein samples for biomarker identification regarding white root disease. The software smoothly handles quite a number of LCMS/MS files (high configuration PC needed) and delivers high quality result. However the current version exports the protein data to excel format, but an additional FASTA format would be much more useful for further analysis. I took one star off for that. It is not a big drawback because FASTA can be generated using external software. As a whole we are satisfied, and are highly dependent on Progenesis QI to carry out shotgun proteomics research. I strongly recommend this software to relevant scientists. "
Status:
ReviewerMember since: 2015
Organization: Ghent University
Application Area:Peptide- and protein-based applications
"For conventional differential proteomics analysis Progenesis QI for Proteomics needs no further ado: it simply works great. We are however currently optimizing its use in label-free analysis of the so-called "histone code", in which thousands of hard-to-identify and complexly modified peptides are simultaneously analyzed. To us, this is where the software opens unprecedented opportunities because it allows us to isolate strongly significant differential peptide ions first and to focus on the manual identification of only the relevant MSMS spectra, instead of all the 160.000 spectra generated over the total dataset that is aligned. The benefit of such Quantify-then-Identify strategies and subsequent targeted acquisition on differential "features" has been nuanced for protein approaches, but it cannot be overestimated when focusing on (modified) peptides."
Status:
ReviewerMember since: 2015
Organization: UNC-Chapel Hill
Application Area:Quantification of proteins by label-free LC-MS/MS
"Progenesis QIP is a great tool for a label-free LC-MS/MS proteomics platform. Very aesthetically pleasing and computationally sound."
Status:
ReviewerMember since: 2014
Organization: Mayo Clinic in Arizona
Application Area:Quantitative Proteomics
"Progenesis QI for Proteomics has helped our users finally perform quantitative proteomics easily. This program is extremely easy to use, and the results have been very reproducible and conclusive."
Status:
ReviewerMember since: 2015
Organization: Utrecht University
Application Area:Analysis of Label free quantitative Proteomics datasets
"With QI the analysis of our large dataset was an almost out of the box no hassle and intuitive experience. Compared to the many (open source) product available working with QI was a breeze. We love the user interface and graphical reports. "
Status:
ReviewerMember since: 2015
Organization: DTU BIosustain
Application Area:Shot gun proteomics of cell lysate
"Using the software has increased the number of identifications obtained."
Status:
ReviewerMember since: 2015
Organization: Univ Milano Bicocca
Application Area:Proteins and endogenous peptides quantitation in tissue and biological fluids.
"We learny how to use Progenesis in few days and then we could go more in-depth of its features with the support of the company. We got positive comments from all groups that are collaborating with us. "
Status:
ReviewerMember since: 2015
Organization: Universidade Estadual do Norte Fluminense
Application Area:Proteomic Analysis
"The software is quite easy to use; it has an intuitive user-interface, and gives us a very reliable high quality analysis. Although easy, it needs some improvements in data refinements so it will be possible to increase data quality. The rate for "After Sales Care" is because, for now, we did not request any customer service. The value paid for the product worth the investment. I would recommend it to others."
Status:
ReviewerMember since: 2006
Organization: UCLA
Application Area:biomarkers of radiation exposure in plasma and bone marrow
"Progenesis QI is proving highly effective for making sense out of complex proteomics datasets from animal tissues. The software is straight forward to use and new personnel can be trained easily. Support is excellent with a clear company focus on building a functional relationship. Value for money is good."
Status:
ReviewerMember since: 2015
Organization: FEderal University of Minas Gerais
Application Area:Proteomic analysis
"The outputs generated by the software are impressive, including the graphic view of the quality controls along the different steps of the proteomic analysis. Congratulations!"
Status:
ReviewerMember since: 2007
Organization: NIH
Application Area:protein expression in tissus samples
"It enables quality comparison of protein expression in samples at different stages"
Status:
ReviewerMember since: 2015
Organization: UCLA
Application Area:Analysis of peptide quantity across heart diseases development
"We used Progenesis for label-free quantification of proteins across a panel of 20+ heart tissue samples. Progenesis took us all the way through the protein quantification pipeline from loading in LCMS data to understanding the statistics of the results. I would highly recommend it to anyone who wishes to focus on the biological questions and not worrying about finding the right software tools."
Status:
ReviewerMember since: 2015
Organization: NUI Maynooth
Application Area:Biomarker Identification
"Very easy to use with excellent help functions and tutorials. After care sales is good and any technical help is straightforward to arrange. The price of the software will be a consideration as other products become available."
Status:
ReviewerMember since: 2014
Organization: Cell Signaling Technology
Application Area:PTM and Total Protein Profiling
"The processing software modules are easy to use and guide you through a step-by-step process for efficient and consistent data processing. The software is versatile with regard to the peak detection, and allows one the flexibility to work within a range of sensible sensitivity settings and provides the tools to survey through the results in a timely fashion. The data browser provides an efficient means to view the results in a thorough and efficient manner, for small and large projects. Overall, I am very pleased with Progenesis QI for my quantitative Proteomics needs. "
Status:
ReviewerMember since: 2014
Organization: UTMB-Galveston
Application Area:proteomics
"Progenesis QI for proteomics has allowed investigators in our department to perform high-quality label-free quantitative proteomics experiments and find interesting targets for follow-up studies."
Status:
ReviewerMember since: 2014
Organization: Cancer Research UK
Application Area:Label-free mass spectrometric quantitation
"This software is now vastly improved compared to earlier versions of the software. The spectral alignments are now more automatic, and easy to verify. Quantitation is accurate and is compatible with data generated from most mass spectrometry vendors. It has a good statistical analysis package. The staff are friendly and very approachable."
Status:
ReviewerMember since: 2014
Organization: Aarhus University (Denmark)
Application Area:Differential proteomics made easy
"Progenesis LC-MS easily complements Waters PLGS and Expression(E) software giving differential expressed proteins in a statistical platform with integrated tools for advanced statistical filtering of proteomics features. Normalization can be customized against spiked features (most abundant spiked peptides) and untargeted differential proteomics can turn into multi-targeted absolute quantification (1). Overall the easy workflow and dynamic change of experiment design combined with the possibility to combine different runs in groups gives the software a higher level of analysis possibility than just the differential proteomics itself. The use of high resolution instruments with ion mobility (IM) features facilitates the software so that the use of HDMSe and Waters Synapt GS2-I has been implemented into Progenesis QI for proteomics in order to take into account also these extra IM features. 1. Christensen JB, Dionisio G, Poulsen HD, Brinch-Pedersen H.(2014) Effect of pH and Recombina"
Status:
ReviewerMember since: 2014
Organization: Aalborg University
Application Area:Proteomics
"Progenesis QI for Proteomics is a quite valuable workflow for LFQ proteomics projects and compatible with most MS instrument platforms. Good value for most Proteomics labs."
Status:
ReviewerMember since: 2014
Organization: CRUK Manchester Institute, University of Manchester
Application Area:Proteomics
"Having used Progenesis LCMS for many years I can confidently confirm it's the most powerful commercial tool for label free proteomics. It's easy to use, has class leading peak detection and produces exceptionally informative stats usually the reserve of advanced informatic packages. An exceptionally valuable tool for high performance label free proteomics."
Status:
ReviewerMember since: 2014
Organization: UNC Chapel Hill
Application Area:Phosphoproteomics
"Progenesis QI for Proteomics is very user-friendly and allows for quick analysis time."
Status:
ReviewerMember since: 2014
Organization: Boston University
Application Area:Proteomics and Biomarker Discovery
"Gold standard for label-free LCMS data analysis across all instrument platforms."
Status:
ReviewerMember since: 2014
Organization: Mayo Clinic in Arizona
Application Area:Quantitative Proteomics
"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."
Progenesis® QI for Proteomics enables you to quantify and identify proteins in your complex samples using the advantages of label-free analysis. With support for all common vendor data formats and a guided workflow, Progenesis QI for Proteomics helps to overcome your data analysis challenges, enabling you to rapidly, objectively and reliably discover proteins of interest from single or fractionated samples.
Solving your analysis challenges
Manufacturer Nonlinear Dynamics | Available Worldwide
4.5 / 5.0 | 40 reviews