"An important factor when performing large-scale de novo sequencing experiments is the ease of use and flexibility of the software. In this respect, PEAKS, being a commercial quality program, was far superior and offered the most adaptive interface, with the ability to import various formats of data from a vast array of mass spectrometers. The sequencing result displayed by PEAKS was also considerably more useful."
"I was amazed to see that PEAKS is extremely well structured! It can be run intuitively. I was absolutely fascinated by the summary page that displays all the statistics. I have never come across anything as helpful as this. Very well done, indeed! .... We would like to expand the data that we get with [our existing software] with PEAKS to get a broader coverage of the proteome. At a first glance, we pull out phosphorylation sites that we would never accept with [our existing software], but since we get a clearcut result with PEAKS, we are certain of looking at correct phosphorylation site. I very much like PEAKS."
"My lab has used several protein identification software products and found that PEAKS is clearly the best: Not only does it produce the most accurate and sensitive results, the graphical user interface is also by far the easiest to use. From loading the raw data to validating and visualizing the final results, PEAKS makes everything so easy."
"... the [PEAKS] results are really excellent as you can see from the number of high confidence PSM and from the narrow mass accuracy distribution...far better of what I could ever squeeze out of my data."
"...the most important thing is that PEAKS is a big time-saver when searching the MS results [...] and that's the big problem we meet in MASCOT."
"The PEAKS program is fantastic. I am obtaining a lot of interesting results for my thesis. I used the program for obtained de novo sequences CID spectra from proteomes of fish that are not represented in the protein database. In addition, I compare the results obtained by PEAKS with the program DeNovoX, which we have in the lab. PEAKS is more specific, has more variable or fixed modifications than DeNovoX, and more possible enzymes (I work with trypsin and Glu-C). PEAKS really is a very good program."
"Thanks a lot, I more and more like the power of PEAKS, it is simply great."
"I have started to use PEAKS Studio and SPIDER(comes within this software) for my research. From the start I could see the potential of the software... I am quite pleased with the guidance and support the team has given me throughout this time, specially one of the members. I can be open with them on the issues I come across, and they reply back with solutions and good background information for me to better understand the software... Thank you for that, and I hope I get to enjoy the improvements of the software."
"We have just downloaded the newest version of PEAKS for a demo. I think that you are breaking the de novo speed limit; it is amazing how fast PEAKS is. Your program is also incredibly accurate. Keep up the good work. Really impressed!"
"Our research has always fought a "battle" against traditional MS/MS protein identification programs in that they were not flexible enough for our application. We look for endogenous peptides that are not cleaved at basic residues (necessarily) and they have multiple PTMs including amidation, acetylation, pyroglutamylation, etc. We don't do tryptic digests, we let our cells do the digesting so to speak, and therefore, other algorithms didn't allow us to search with the flexibility that PEAKS allows. Now we can identify our endogenous peptides with ease."
"PEAKS has helped us to identify unmatched results or confirm ambiguous sequences found by standard database searching methods. As a whole, the sequence coverage increased dramatically for some of the proteins under investigation."
"I am so happy with PEAKS, it is outstanding! It is so much better, easier, faster than [other software]..."
"We believe that PEAKS Studio 5.3 software is now a complete and powerful software package. It is now our reference software."
Here are some with specific reference to the SPIDER application:
"My compliments to you for your interesting and useful program SPIDER".
"I'm a big SPIDER fan!"
"The results I've been getting have been consistently very good. Thank you for this great piece of software!"
"Your software is by far the fastest and more user-friendly I have found."