Progenesis QI for Proteomics by Nonlinear Dynamics

Manufacturer Nonlinear Dynamics  |  Available Worldwide
4.5
/
5.0
  |  33 reviews
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 QC metrics to evaluate the qualit... Read more


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Progenesis QI for Proteomics

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Average Rating: 4.5
33 Scientists have reviewed this product

5 out of 5
Ease of use
5 out of 5
After sales service
4 out of 5
Value for money


Great data analysis tool for label-free proteomics
Rating: 4.3

  • Application Area: shotgun proteomics, label-free

"Easy to use (step by step approach), excellent tutorial and support, nice visualization of data"

Review date: 11 Jul 2018 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2013

  • Organization: Iuliu Hatieganu University of Medicine and Pharmacy Cluj Napoca



  • Ease of use
    4 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Great results.
Rating: 4.7

  • Application Area:Shotgun label free proteomics

"Very useful tool for comparative evaluation of proteomic data."

Review date: 06 Jul 2018 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2018

  • Organization: King Adbullah University of Science and Technology



  • Ease of use
    5 out of 5
    After sales service
    4 out of 5
    Value for money
    5 out of 5
A good tool to use for Label-Free quantitation.
Rating: 4.7

  • 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."

Review date: 06 Jul 2018 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2018

  • Organization: Functional Genomics Center Zurich



  • Ease of use
    5 out of 5
    After sales service
    2 out of 5
    Value for money
    3 out of 5
Good product for newbie user.
Rating: 3.3

  • 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."

Review date: 06 Jul 2018 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2018

  • Organization: University of Helsinki



  • Ease of use
    4 out of 5
    After sales service
    2 out of 5
    Value for money
    4 out of 5
Lovely piece of analytical software.
Rating: 3.3

  • Application Area:Proteomics

"Results are consistent and software us powerful. updates useful for the user, so software is developing to the way users want."

Review date: 06 Jul 2018 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: Ghent University



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    4 out of 5
Progenesis QIP allows us to catch a glimpse of peptide emergence in proteomics
Rating: 4.7

  • 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."

Review date: 05 Jul 2018 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2018

  • Organization: Medicago



  • Ease of use
    4 out of 5
    After sales service
    5 out of 5
    Value for money
    4 out of 5
Great results, fast process.
Rating: 4.3

  • 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."

Review date: 05 Jul 2018 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2018

  • Organization: Centro Cardiologico Monzino IRCCS



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    4 out of 5
Good and fast results.
Rating: 4.7

  • 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."

Review date: 19 Feb 2018 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: University of Maryland, School of Pharmacy



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Progenesis QI for proteomics is an efficient and robust platform for proteomic data analysis.
Rating: 5.0

  • 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."

Review date: 09 Sep 2016 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: Mayo Clinic in Arizona



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Progenesis QI is a no-brainer for label-free quantitative proteomics.
Rating: 5.0

  • 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."

Review date: 02 Sep 2016 | Progenesis QI for Proteomics


  • Status:

    Reviewer

  • Member since: 2016

  • Organization: University of Leicester



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Very flexible bit of software form biomarker discovery
Rating: 5.0

  • 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."

Review date: 02 Sep 2016 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: Tun Abdul Razak Research Centrel



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    4 out of 5
Rating: 4.7

  • 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. "

Review date: 26 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: Ghent University



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    4 out of 5
Rating: 4.7

  • 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."

Review date: 14 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: UNC-Chapel Hill



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Rating: 5.0

  • 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."

Review date: 10 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: Mayo Clinic in Arizona



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Rating: 5.0

  • 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."

Review date: 10 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: Utrecht University



  • Ease of use
    4 out of 5
    After sales service
    5 out of 5
    Value for money
    4 out of 5
Rating: 4.3

  • 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. "

Review date: 06 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: DTU BIosustain



  • Ease of use
    4 out of 5
    After sales service
    3 out of 5
    Value for money
    4 out of 5
Rating: 3.7

  • Application Area:Shot gun proteomics of cell lysate

"Using the software has increased the number of identifications obtained."

Review date: 06 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: Univ Milano Bicocca



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Rating: 5.0

  • 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. "

Review date: 05 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: Universidade Estadual do Norte Fluminense



  • Ease of use
    4 out of 5
    After sales service
    3 out of 5
    Value for money
    5 out of 5
Rating: 4.0

  • 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."

Review date: 05 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2006

  • Organization: UCLA



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    4 out of 5
Rating: 4.7

  • 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."

Review date: 05 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: FEderal University of Minas Gerais



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Rating: 5.0

  • 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!"

Review date: 05 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2007

  • Organization: NIH



  • Ease of use
    4 out of 5
    After sales service
    4 out of 5
    Value for money
    3 out of 5
Rating: 3.7

  • Application Area:protein expression in tissus samples

"It enables quality comparison of protein expression in samples at different stages"

Review date: 05 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: UCLA



  • Ease of use
    5 out of 5
    After sales service
    4 out of 5
    Value for money
    5 out of 5
Rating: 4.7

  • 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."

Review date: 05 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2015

  • Organization: NUI Maynooth



  • Ease of use
    4 out of 5
    After sales service
    4 out of 5
    Value for money
    3 out of 5
Rating: 3.7

  • 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."

Review date: 05 Aug 2015 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: Cell Signaling Technology



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Rating: 5.0

  • 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. "

Review date: 25 Sep 2014 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: UTMB-Galveston



  • Ease of use
    5 out of 5
    After sales service
    3 out of 5
    Value for money
    4 out of 5
Rating: 4.0

  • 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."

Review date: 23 Sep 2014 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: Cancer Research UK



  • Ease of use
    4 out of 5
    After sales service
    5 out of 5
    Value for money
    3 out of 5
Rating: 4.0

  • 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."

Review date: 22 Sep 2014 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: Aarhus University (Denmark)



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Rating: 5.0

  • 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"

Review date: 18 Sep 2014 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: Aalborg University



  • Ease of use
    4 out of 5
    After sales service
    5 out of 5
    Value for money
    4 out of 5
Rating: 4.3

  • 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."

Review date: 16 Sep 2014 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: CRUK Manchester Institute, University of Manchester



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    4 out of 5
Rating: 4.7

  • 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."

Review date: 16 Sep 2014 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: UNC Chapel Hill



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Rating: 5.0

  • Application Area:Phosphoproteomics

"Progenesis QI for Proteomics is very user-friendly and allows for quick analysis time."

Review date: 16 Sep 2014 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: Boston University



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Rating: 5.0

  • Application Area:Proteomics and Biomarker Discovery

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

Review date: 16 Sep 2014 | Progenesis QI for Proteomics
  • Status:

    Reviewer

  • Member since: 2014

  • Organization: Mayo Clinic in Arizona



  • Ease of use
    5 out of 5
    After sales service
    5 out of 5
    Value for money
    5 out of 5
Rating: 5.0

  • 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."

Review date: 16 Sep 2014 | Progenesis QI for Proteomics

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

  • QC metrics to evaluate the quality of your LC-MS data.
  • Consistent peak peaking across all runs, vital for accurate and precise quantification, using our unique approach to co-detection of peptide ions.
  • Compatible with 1D and 2D-LC and no restrictions on the number of groups, samples or experimental designs you can compare within your analysis.
  • Complete data matrix and no missing values for reliable multivariate statistics.
  • Query Data bases using common search engines to automatically combine identifications with peptide ion quantification data.
  • Fully compatible with ion mobility to achieve three dimensions of resolution.
  • Powerful data visualizations and guided workflow for DIA and DDA analyses.
  • Easy export to Pathway Analysis tools to aid biological understanding of discoveries.