Running SEQUEST from Qual Browser vs. SEQUEST Browser
Where should you run SEQUEST?
You can run SEQUEST from either the Qual Browser application or from Bill Lane's SEQUEST browser. So where should you run SEQUEST? I really like the SEQUEST browser when I want to produce results from an entire chromatogram. I like to use SEQUEST from Qual Browser when I just have a few spectra to search (a quick and dirty mode). I may just "cherry pick" a few spectra and SEQUEST from Qual Browser while a run is still going to get an idea of what I'm looking at (hopefully not all keratin, yikes). The SEQUEST browser puts a web front end on the entire process of setting up, running, and managing your SEQUEST results. Managing the results into specific directories really helps to keep things in order. You also get many more tools within the SEQUEST browser, like the fuzzy ions denovo sequencing tool, FASTA Maka for creating database files, DTA VCR, Ion QUEST and many more.
If you work in big pharma, or any other large organization with a bloated informatics department, one caveat of the SEQUEST browser is that you need to install a webserver on your instrument (or wherever you want to serve up the data). This means you may have to talk to your IS department and get their "permission" which could take years and cost thousands of lives (no cynicism here, just kidding). But go ahead, bite the bullet, it is well worth it. I had this set up at BMS so I could just point my collaborators to a URL to retrieve their results. One note of caution: you may still may have to educate your collaborators as to what all of the SEQUEST output means. Might I suggest Sequest tips? Have fun!
 
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