If you would like to add your feedback to our list, please contact us.

Here is a sample of what users have to say about Phenyx:

---

"Using the search software SEQUEST for a year in my lab made me long for something less cumbersome to use. Naturally, there's Mascot as an alternative. Since recently, there's another alternative: Phenyx. Constantly searching for something better, we tried it out after having registered as a user at http://phenyx.vital-it.ch/pwi. What I like with Phenyx is that it is entirely Web-based. One major problem core labs have is to distribute the results in a suitable manner. Due to the enormous amount of data generated by current instruments, results must be communicated electronically. Phenyx offers this possibility so that each user can access the results individually and eleborate on them to their liking."

"I am particularly attracted by the clearly arranged main page of Phenyx where one sees the search ID, user and status of the searches submitted. The protein overview is the main gate to have a look at the actual search results that leads then further to the identified peptides and MS/MS spectra that can be accessed by the individual peptides. What I like in particular is the colour-coded display of the ions in the MS/MS spectrum. Everyone who needs to dwell on such spectra knows when to call a spectrum a good one or a bad one; with Phenyx's colour-coded display, one gets a nice visual impression without looking at the actual spectrum."

"These are just some features I like in particular about Phenyx. As always one needs to work with the software to not just scratch the tip of the iceberg. Again, as a user who is somewhat tired of SEQUEST, I was instantly attracted by the simplicity and clarity of Phenyx. As always, there are some features that should be added. For example, proteomics is getting quantitative. Quantitation is not yet included, but I'm sure future releases will include this option."

Dr. Paul Jenö
Department of Biochemistry
Head of Mass Spectrometry Services
Biozentrum of the University of Basel
Switzerland

 

"I am involved in different proteomic-based projects using MALDI tandem time-of-flight mass spectrometry and quantitative proteomics. Although the mass accuracy of those instruments is relatively high when compared to ion-trap based instruments, a robust peptide identification tool is necessary for optimal performance. For several reasons, the Phenyx database search platform fits exactly my needs in this domain."

"First, the tool provides robust and sensitive results. The ability to rapidly estimate false positive and false negative ratios is particulary useful at this stage, and limits in a very efficient manner any kind of manual input as well as any bias resulting from "manual validation" (which is de facto a subjective field). In addition, several utilities and an excellent graphical interface make the tool user friendly and easy to use."

"Second, the integration of the Phenyx platform in the analytical pipeline is very efficient. Indeed, the tool is compatible with all common input formats, including the recent standards mzXML and mzData. The results are then easily exported in the form of tables and reports. At this stage, the ability to export various parameters such as precursor intensity or reporter ion intensity (in the case where isobaric tags are used) associated with identified peptides allows a quick, simple and efficient coupling between the qualitative tool (the database search engine) and the quantitative aspect of the study. This latter point is of particular importance, since compatibility between the different steps is generally the most limiting factor, and therefore mandatory in this field."

Dr. Alexander Scherl
Research Associate
Goodlett Lab
Dept. of Medicinal Chemistry
University of Washington
USA

 

"We have different proteomics-oriented projects running in our laboratory using an ion trap mass spectrometer with a limited mass precision and low resolution. The Phenyx peptide identification algorithm has been designed to deal with this kind of data."

"During all the years I have used it so far, the database search results convinced me again and again. As the calculated peptide scores are of true probabilistic nature, it takes only a couple of LC-MS/MS runs to find out which scoring threshold results in true positive identifications (quality of MS/MS spectra is related to the instrument used). We have validated the ruggedness of the Phenyx scoring in a recent publication [Heller M. et al (2005) J. Proteome Res. 4, 2273]. This performance makes the validation of identification results an easy task, even if one has to deal with many different samples of unknown composition (keyword: shotgun proteomics). Additionally, the Web-based user interface provides many possibilities, which enables us to adapt each database search very specifically to our needs. Furthermore, the results can be displayed in a lot of different ways, which helps enormously for results validation and comparison."

Dr. Manfred Heller
Department of Clinical Research
University of Bern
University Children's Hospital, G3-844
Switzerland

 

"Our laboratory is involved in the identification of potential cancer biomarkers, which are then combined in specific protein patterns. A current problem with protein biomarker identification strategies is that the probability of obtaining unambiguous identification by MS/MS decreases when relatively low amounts of protein are available or when potential biomarkers are found mixed with other proteins. Moreover, each identification has a cost. But it is difficult to limit this cost (using for instance an ion trap) while improving the accuracy of peptide fragment mass measurements."

"We thought that one solution could be to use software packages that do not use essentially the precision of mass measurements to increase the confidence of protein identification. Then, for the identification of possible breast cancer protein biomarkers, the MS/MS spectra previously analyzed with a current software package were also analyzed with Phenyx. Both packages provided more or less similar protein identification. Nonetheless, in several cases the identified peptides and their number differed, the sequence coverage being increased by merging the information obtained by both software packages. Moreover, several proteins with a low number of peptide fragments, and low concentration components of protein mixtures that did not give a significant score with the current package, were undoubtedly identified using Phenyx."

Dr. Michel Caron
Director, Protein Biochemistry and Proteomics Laboratory
UPRES EA 3408 Immunopathologie et ImmunoIntervention
UFR SMBH Léonard de Vinci
Université Paris 14
France

 

"The software algorithm is quite good and there are some useful and convenient features such as 1) being able to save all searching results in the software, 2) being able to search multiple data files and different data format files, 3) being ablee to reject/accept a protein ID, 4) being able to export results as a table in Excel/XML/text file."

Mai-Loan Huynh
Project Scientist
Minomic Pty Ltd
Australia

 

"I want to make my compliments to the Phenyx development team for their work on the Linux version. I am a long time Debian user and I have particularly appreciated the full Debian-style installation procedure. It's not usual for commercial products."

Renzo Bagnati
Instrumentation Analytics
The Mario Negri Institute for Pharmacological Research
Italy

 

"I must say I liked the LIMS interface of Phenyx and found it more intuitive than any other proteomics LIMS I have used. The data import and results export functions are directly accessible and supports a range of common file formats which makes it very easy to use Phenyx with other software."

Dr. Magnus Palmblad
Senior Research Fellow
The Biocentre
University of Reading
United Kingdom

 

"The last two days I played around with Phenyx and I have to admit that I like it more and more, mainly because of its flexibility and also because of the nicely organized Excel tables I can get. I also like the result comparison page."

Dr. Gabriella Pocsfalvi
CESMA-PROBIO
Proteomic and Biomolecular Mass Specrometry Center
Institute of Food Science and Technology, C.N.R.
Italy

 

"Phenyx is a great software, much better than Mascot. I am confident on two things: 1: Phenyx will become a very popular programme in the future for proteomic applications all over the world; 2: I will be able to publish one or two journal papers soon based on my Phenyx data analysis results to spread the great name worldwide: PHENYX!"

Dr. William Yang
PhD Student
Centre for Green Chemistry
School of Chemistry, Faculty of Science
Monash University
Australia

 

"My feeling of the software so far is that it does a very good job indeed! First of all it is very user-friendly with the result-comparison view and so on. Second, as to the quality of the IDs I find it to be at least as good as the ProteinLynx Global Server 2 (PLGS2.2), which I am currently using. The data is being generated on a Waters/Micromass QTOF Ultima Global instrument. From the same data, there is a rough 75% overlap of the identifications using PLGS2 and Phenyx. The trend is that the IDs that differ cluster among the lower probability identifications. Third, I find that the valid peptides (peptide scores >6.0? =default settings) seem to be good matches for the vast majority (>97-98%) of cases. This is excellent."

"As for myself and the comparison with X!Tandem and PLGS2, it turns out that the highest number of shared IDs is between Phenyx and PLGS2, with Phenyx identifying slightly more peptides using default parameters. I very much appreciate the ease of viewing and comparing results in Phenyx; there it clearly outperforms PLGS2."

Dr. Johan Lengquist
Karolinska Biomics Center (KBC)
Karolinska University Hospital
Sweden

 

"What attracts me to Phenyx is the common sense approach and I really like the mass accuracy profiles it gives as it's a great way of monitoring the analyses and of comparing different instruments."

"The PWI is nicely streamlined and I like it."

Dr. David Knight
Senior Experimental Officer
Faculty of Life Sciences
University of Manchester
United Kingdom

 

"I must admit I was quite impressed by Phenyx, and particularly like the way you could access previous submissions, and export them to Excel. It was also much faster than our in-house Mascot server."

Dr. Stuart Cain
Research Associate
Faculty of Life Sciences
University of Manchester
United Kingdom

 

"One of the best things about Phenyx is that it accepts most types of MS/MS peak lists. In our lab I have so far used Finnigan Dtas, Micromass Pkl and Mascot generic from ABI (tmp I use to combine spectra from different runs of 2d-LC-MS analysis and then analyze at once in Phenyx)."

"Phenyx is so far the best algorithm I have used to group peptides into protein hits. In my analyses of Trypanosoma cruzi subproteomes, we found several members of multigenic families, such as trans-sialidase, gp63 and MASP and Phenyx was the one that best grouped the peptides into protein hits."

Dr. Ernesto Yakayasu
Dept. of Biological Sciences
University of Texas at El Paso (UTEP)
USA

 

"I really like Phenyx as it allows more DTA submissions than Mascot can handle. I also like the fact that it stores all my submissions and allows me to check back on things."

Karen Hegney
University of Edinburgh

 

"Phenyx has the greatest number of innovative, forward thinking, unique features of any sequence search engine that we have found. The ability to compare proteomic runs should have been a basic function from the start in proteomics; however, Phenyx is one of only several search engines that has incorporated this functionality."

Andrew Guzzetta
IonSource

 

"I browsed your website to get an idea of the potentiality of Phenyx, and in general I am favourably impressed."

Antonio Masi
Researcher
University of Padova
Italy

 

"I preferred Phenyx to Mascot due to its deep and easy PDF manual. Moreover I liked the fact that the user can keep previous results and find them on the Web any time and the possibility to launch many submissions at the same time and login again later to collect the results."

Paolo Carletti
PhD Student
Dept. of Agriculture Biotechnology
University of Padova
Italy