Proteomic Database Search and Analytical Quantification

As the field of proteomics matures and operation of mass spectrometers using standardized methods becomes more user-friendly, an increasing number of chemists and biologists are becoming involved routinely in designing and executing proteomic studies, followed by data analysis and interpretation. It has become apparent that it is essential for biologists and chemists to have an in-depth understanding of the computational tools used in database searching, statistical significance determination, and other processes in data compilation. With very few exceptions, software for database searches gives the investigator power to set search parameters. Some software is equipped with tools for statistical analysis, particularly quantitative measurements. Therefore, this chapter aims at providing the “working knowledge” necessary for research scientists, who are not proteomics experts, to understand how to process, analyze, and interpret mass spectrometry data.

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