PEAKS User Community: Comment Post

De Novo Sequencing

Protein ID

PTM

Seq. Tag Search

User Community

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Current Community Postings:

2007-11-13

PEAKS User

PEAKS

Ana Pereira

My experience with Peaks and the Bioinformatic Solutions' team has been quite interesting. I have started to use Peaks Studio 4.5 and Spider (comes within this software) for my research. From the start I could see the potential of the software, but took me sometime to go about the results. However, 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. We agree that there are some issues yet to be resolved, but they have taken not only my suggestions already, but are interested to keep working with me to solve my specific needs. Thank you for that, and I hope I get to enjoy the improvements of the software.

2006-01-10

PEAKS User

PEAKS

Andrew Guzzetta

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! Sincerely, Andrew Guzzetta IonSource.com

Yes, we should be able to de novo sequence peptides faster than the MS/MS can spit them out.

2005-11-23

PEAKS User

PEAKS

Timothy Richmond

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.

2005-11-15

PEAKS User

PEAKS

Christian

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. [download 254.278 Kb]

2005-11-15

PEAKS User

PEAKS

Kari

"I am so happy with PEAKS, it is outstanding! It is so much better, easier, faster than [other software]..." - Dr. Kari Green-Church, Associate Director CCIC Mass Spectrometry and Proteomics Facility, Ohio State University [download 360.38 Kb]

2005-09-30

Development

PEAKS

IainR

I'm posting just to start things off. There's lots of things happening with PEAKS these days and the new developments will be exciting. Anybody have anything they really like about recent developments, or anything they'd like to see in the future?