Unrestricted Search Tutorial

Unrestricted Search Tutorial Sam Payne Winter 2007 This tutorial explains the unrestricted search option of Inspect (Tsur 2005, Tanner 2008), and assumes a completion of previous Inspect tutorials. An unrestricted search is a powerful tool for finding evidence of post-translational modifications in MS/MS spectra. Rather than identifying only specified modifications, an unrestricted search finds peptides with any PTM (up to a size limit). Using this feature properly requires an understanding of several practical and technical issues. • Database • Inspect Commands • Inspect Run • Post-Processing This will not cover all the features of an unrestrictive search, but enough so that you can successfully run the search. Additional information can always be found in the documentation included in the Inspect folder “docs.” Introduction: There are now two papers explaining the theory of both the search and the post-processing for the unrestrictive searches. I suggest that you read both of those, cited at the end of the tutorial. There are a few things that I need to explain. First, the unrestrictive search is has the best power on large samples, more than 100,000 spectra. If you read the Tanner paper you will see that we do a lot of statistics based that are helped by big numbers. If you have a single dataset of 10,000 spectra (of which only 20-30% have annotations), then you might not find what you’re ...