I work for a company called Bioinformatics Solutions and we are the creator of PEAKS Software. You may have heard of us before as we have the top de novo sequencing algorithm on the market. Our program also includes a meta search protein ID called inChorus which can directly launch 5 db search engines within PEAKS (PEAKS, X!Tandem, OMSSA, Mascot and Sequest) and give you back all the results in one coverage report without transferring data files or leaving your computer.
We also have a tool called SPIDER which is a better than Blast-like homology search tool that can be used to increase your protein ID coverage by at least 20%, after you have completed a de novo and db search and will build the correct peptide sequence from these results.
We are compatible with all types of fragmentation and are able to combine data that has been generated using multiple types of fragmentation. PEAKS can be used with almost any instrument data and reads many RAW file formats.
Finally, PEAKS can be installed and get you data results within 20 minutes of installation. It's that easy to use!
I hope to hear from you soon,
Janine Voyer, MSc