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Data Analysis for Mass Spectrometry-Based Proteomics
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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.
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