Users Making News

Nilesh Tannu and Scott Hemby of Wake Forest University have published their De novo protein sequence analysis of Macaca mulatta paper in BMC Genomics. Their work overcomes the limitations of proteomics studies on Rhesus monkey, which has a limited sequence database, by using PEAKS de novo sequencing in conjunction with SPIDER homology searching. While traditional searching identified some proteins, they were able to identify many more peptides, and saw a dramatic gain in the number of reasonable proteins identified. Rhesus monkey will become important in various neuropeptide studies, as a model for the human brain. [more]

Software Upgrade Announcement

As of November 12th, 2007, the PEAKS team released the following software:

• PEAKS Online 2.0
• PEAKS Client 4.5
• PEAKS Viewer 4.5
• PEAKS Studio 4.5 sp2

Ideal as a shared resource, this latest release of PEAKS Online, the high throughput webserver/cluster, now includes industry grade security and user management. System administrators can empower users and research groups to share resources without compromising security. PEAKS Online provides a forum for efficient collaboration. Free trial users can process multiple tests at once by harnessing the powerful PEAKS public server. Load in a private or public database and see the results on your own data using built-in and customizable enzymes and modifications. Be among the first to investigate this new tool at no charge. Sign up for PEAKS Online at www.bioinfor.com/peaksonline.

Connect PEAKS Online with the new PEAKS Client. You can read RAW data and submit batches of searches, inChorus meta search (automatically compare results with Mascot, Sequest, X!Tandem, etc), do manual de novo sequencing or find homologous peptides using SPIDER. Or just send results to a friend along with a copy of PEAKS Viewer.

With the new PEAKS Studio 4.5 SP 2, users will see more flexible import of Mascot results, and even better filtering features. Try the Retention Time Prediction tool!

Attention iTRAQ users!

We're addressing some tough questions: What happens when all your peptide ratios support a certain protein ratio, except one? How much should you trust a peptide ratio from a less intense spectrum? What do you do when you have a ratio for a peptide, but it doesn't match to a protein? Why isn't anyone else addressing these questions?!

The PEAKS team plans to release our iTRAQ, ICAT, SILAC, and no-label quantification software next year. The algorithms are already written, and they're ready to be tested on real data. Anybody want a sneak preview? We've already had some fantastic interest so far, but we'll only get better if we participate in as many studies as possible. Send us your data and we'll do the analysis for you, and give you a pre-release version of the software.

PEAKS Development

To keep on top of the latest developments in PEAKS, and to take advantage of the newest PEAKS tools visit www.bioinfor.com/peaks.php or contact your sales rep today.