Which Database to Use?—Confusions and Puzzles in Database Search and Sequence Analysis—

Abstract

For mass spectrometry based-proteomics studies, computational analyses of obtained data are indispensable. However, the analysis methodologies and software for mass spectrometry and/or proteomics are currently still under development and many problems thus remain unfixed; consequently, researchers, especially experimental scientists, often suffer from technical issues and popular misinterpretations. Based on these problems, we describe in this review the computational processes for protein identification for proteomics beginners, especially the algorithms of database search and related basic issues: the comparison of de novo sequencing method and database search method, the effects of PTM detection on the search results, an overview of life science databases, and tips and cautions for their application to database searches.