Seattle Proteome Center (SPC)
NHLBI Proteomics Center at the Institute for Systems Biology

PROTEOMICS INFORMATICS COURSE AT ISB

The objective of this course is to instruct active proteomics researchers in the use of a suite of software tools -- a transproteomic pipeline (TPP) -- designed for the analysis, validation, storage and interpretation of data obtained from large-scale quantitative proteomics experiments using the ICAT reagent labeling method, multi-dimensional chromatography and tandem mass spectrometry. Through lectures and hands-on exercises, each course participant should become proficient in the use of the tools.

Prerequisite for participation in the course is a demonstrated understanding in the operation of tandem mass spectrometers, the basic structure and interpretation of peptide MS/MS spectra and proficiency in the use of computers. A commitment to attend all five days of the course is also required.

The next course is tentatively scheduled for early November, 2008. Applications will be accepted beginning July; accepted participants will be notified and will receive instructions on how to register. Registration will be considered complete upon receipt of registration fee. If you would like to be notified of future sessions or have any other questions please contact the Center.

May 2008 Lectures

• Day 1 - Intro to Mass Spectrometry Based Proteomics Workflow - Dan Martin
• Day 1 - MS/MS Database Searching - Jimmy Eng
• Day 1 - Graphical User Interface for the TPP - Luis Mendoza
• Day 1 - Pep3D, Data Formats and Converters - Josh Tasman
• Day 1 - TPP Installation & Support - Luis Mendoza
• Day 2 - PeptideProphet: Validation of Peptide Assignments - Andrew Keller
• Day 2 - Qualscore - Luis Mendoza
• Day 2 - Discovery and Validation tools for Biomarker Research: Introduction to Corra and TIQAM - Mi-Youn Brusniak
• Day 3 - ProteinProphet: Statistical Validation of Protein Identifications - Alexsey Nesvizhskii
• Day 3 - SpectraST: A Spectral Library Searching Tool for Proteomics - Henry Lam
• Day 4 - The Study of Macromolecular Complexes by Quantitative Proteomics - Jeff Ranish
• Day 4 - Quantitation with Xpress - David Shteynberg
• Day 4 - Isotopic Labeling and MS-based Quantitative Proteomics - David Shteynberg
• Day 4 - iTRAQ Quantitation with Libra - Luis Mendoza
• Day 5 - SBEAMS – Proteomics & PeptideAtlas Database - Eric Deutsch
• Day 5 - Gaggle: Loosely-coupled Software for Data Visualization - Christopher Bare
• Day 5 - Trans-proteomic Pipeline: Exploring for Protein Function - Hector Ramos