Progenesis QI for Proteomics by Nonlinear Dynamics

"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."

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

"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."

"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."

"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."

"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."

"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."

"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."

"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. "

"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."

"Progenesis QIP is a great tool for a label-free LC-MS/MS proteomics platform. Very aesthetically pleasing and computationally sound."

"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."

"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. "

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

"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. "

"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."

"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."

"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!"

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

"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."

"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."

"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. "

"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."

"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."

"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"

"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."

"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."

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

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

"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."