2010 Fall Workshop:  Carbohydrate Analysis

Program information is not yet available.

 

2009 Fall Workshop Program:

Bioinformatics for Protein Identification

Co-Chairs: John Cottrell, Matrix Sciences and Karl Clauser, Broad Institute

November 5 - 6, 2009, Baltimore, MD  

Thursday, Nov. 5	Friday, Nov. 6
8 am: Workshop Registration 8:30 am – 12:15 pm: Session 12:15 – 2 pm:  Lunch 2– 5 pm:  Session	8:45 am – 12:15 pm:  Session 12:15 – 2 pm:  Lunch 2 – 5 pm:  Session

Protein identification and characterisation by database searching is a well-established technique, contributing to more than 1000 peer reviewed publications each year. Data interpretation from such experiments is non-trivial because real MS/MS spectra are not ideal transformations of peptide sequences. A real mass spectrum has finite resolution and finite signal to noise ratio, mass spectrometers have limited mass accuracy, peptide precursor ions rarely dissociate into complete fragment ion series, enzymes cleave proteins with imperfect fidelity, and typical sample handling can induce chemical artifacts.

The 2009 Fall Workshop will begin with an introduction to the subject, then move on to explore key topics in greater depth. While mathematics and statistics cannot be avoided completely, presentations will emphasise practical matters, aiming to answer questions such as: What software tools are available? Which sequence database should I choose? What is the confidence level of the identifications in a dataset? How do I find post-translational modifications? What are q-values and p-values? How can I comply with publication guidelines?

 

Presentations by experts will be complemented by hands-on exercises, ranging from manual interpretation of an MS/MS spectra to figuring out the correct search parameters for some real data files.

 

Agenda:

The Workshop will begin with registration at 8:00 AM on Thursday, November 5.  Lunch is included on both Thursday and Friday, November 5 and 6.  The program will conclude by 5:00 pm on Friday.  For hands-on experience, it is recommended that registrants bring a laptop computer.

 

Speakers:

Introduction - John Cottrell, Matrix Science

Searching Uninterpreted MS/MS Data - Jimmy Eng, University of Washington

Alternative Strategies - David L. Tabb, Vanderbilt University

Sequence Databases - Akhilesh Pandey, Johns Hopkins University

Modifications - Karl Clauser, Broad Institute 

Data Reduction and Transformation - Manor Askenzai, Harvard University

Validation and Statistics - Michael MacCoss, University of Washington

Reporting - Brian Searle, Proteome Software