Sunday, March 7, 2010, 9:00 am - 4:00 pm (with one hour break for lunch-on-your-own)

Instructors:  Richard Chalkley (UCSF), Rachel Orgorzalek Loo (UCLA), Katalin F. Medzihradszky (UCSF), and David Tabb (Vanderbilt)

Course description

Not all protein sequence information is available in databases.  Organisms with unsequenced genomes or with unanticipated protein, RNA, or DNA processing may require tandem mass spectra to be interpreted, rather than fit to predicted spectra.  In addition, not all database search results are reliable, so an ability to independently determine the reliability of a match is an important skill.

 

This course will discuss principles of gas phase peptide dissociation and ion activation.  It will then train attendees in manual interpretation of spectra. It will also review publicly available software for partial and full automatic interpretation of sequence directly from MS/MS ions.  This review will include de novo algorithms such as PepNovo and sequence tagging algorithms such as InsPecT and DirecTag, programs which can supplement data analysis by interpreting high-quality spectra that resist database identification.  Use of both collisional induced dissociation and electron capture/transfer dissociation will be presented. Post-translational and artifactual modifications and their impact on spectra will also be discussed, along with useful derivatization strategies to aid interpretation.  Manual interpretation will be an important component of this course.  Participants are encouraged to bring a calculator.

 

 

Tuition:  $150