MassSpec research

This will hold the stuff for my mass spec research with Carl Ebeling as my advisor.

2/15/06

So now its downloading XTandem, figuring out what's going on there and waiting for some example data from John. Though I should have plenty to do in figuring out XTandem without the data . .. .

Meeting with Carl and John 2:00 on Friday. Don't forget.

Papers from John Keane

he safest and quickest route to get started is probably to accelerate the "search" process (like the Toronto team did), based on the popular open-source algorithm in the "X!Tandem" program. Here are a few links to how it works:

X! Tandem flow chart (Not yet useful)

Open source system for analyzing, validating, and storing protein identification data. (Useful soon I think) Related papers.

TANDEM: matching proteins with tandem mass spectra. (Not yet useful) Related papers.

Hardware-accelerated protein identification for mass spectrometry (Useful)

Short analysis of the Toronto work on some blog (Not useful yet)

Other pages

The Global Proteome Machine Organization (Tons of open-source code to validate designs and such)

A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes (Sounds useful)

Literature References for The GPM Project (literary references are always good)

Designing hardware for protein sequence analysis (sounds related)