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.

Lecture slides from the April 27-May 1, 2009 course can be viewed via the links below. Though the next session is not yet planned, you are welcome to leave your name by filling out a brief application ; you'll be notified when new course dates are established. If you have any other questions, please feel free to contact the Center.

Day 1 Lectures

• Mass spectrometry Based Proteomics Workflow -- Dan Martin
• MS/MS Database Searching -- Jimmy Eng
• GUI -- Luis Mendoza
• Database Searching Tutorial -- Eng, Mendoza
• Data Formats and Conversion -- Natalie Tasman
• Data Formats Tutorial -- Tasman
• Installation -- Luis Mendoza

Day 2 Lectures

• PeptideProphet -- Andrew Keller
• PeptideProphet Tutorial -- Keller
• Qualscore -- Luis Mendoza
• InterProphet -- David Shteynberg
• InterProphet Tutorial -- Shteynberg

Day 3 Lectures

• ProteinProphet -- Alexey Nesvizhskii
• ProteinProphet Tutorial -- Nesvizhskii
• SpectraST -- Natalie Tasman
• SpectraST Tutorial -- Tasman

Day 4 Lectures

• The Study of Macromolecular Complexes by Quantitative Proteomics -- Jeff Ranish
• XPRESS and ASAPRatio -- David Shteynberg
• EXPRESS and ASAPRatio Tutorial -- Shteynberg
• Libra -- Luis Mendoza
• Libra Tutorial -- Mendoza
• Corra and TIQAM -- Mi-Youn Brusniak
• TIQAM Tutorial(s) -- Brusniak

Day 5 Lectures

• SBEAMS Proteomics and PeptideAtlas -- Eric Deutsch
• SBEAMS_Peptide Atlas Tutorial -- Deutsch
• Gaggle -- Christopher Bare
• PIPE -- Hector Ramos
• PIPE Tutorial -- Ramos