Data Analysis for Mass Spectrometry-Based Proteomics

Tandem mass spectrometry is one of the most important
tools for protein analysis. This work is focused on
the development of new methods and algorithms for
tandem mass spectrometry data analysis. A database
search engine, MassMatrix, has also been developed
that incorporates these methods and algorithms. The
program is publicly available both on the web server
at www.massmatrix.net and as a deliverable software
package for personal computers. Three different
scoring algorithms have been developed to identify
and characterize proteins and peptides by use of
tandem mass spectrometry data. In addition, a data
analysis method for identification of disulfide bonds
in proteins and peptides by tandem mass spectrometry
data has been developed and incorporated in
MassMatrix. By this new approach, proteins and
peptides with disulfide bonds can be directly
identified in tandem mass spectrometry with high
confidence without any chemical reduction and/or
other derivatization.