"Mass Spectrometry Data Analysis in Proteomics" is a comprehensive textbook that addresses the theory and practice of analyzing raw data from mass spectrometry in the field of proteomics. Given the high throughput capacity of mass spectrometry techniques, it is essential for researchers in proteomics to engage deeply with data analysis. This book provides a detailed overview of available bioinformatics programs, algorithms, and databases that can be used for mass spectrometry data analysis. General guidelines for data analysis using search engines such as Mascot, Xtandem, and VEMS are provided, with a particular focus on identifying low-quality data and optimizing search parameters. Additionally, various types of mass spectrometry data are discussed, and optimal methods for converting raw data into peak lists suitable for input into search engines are described. The selection of the most accurate and comprehensive databases is emphasized, and a report on available sequence databases is provided. The book also describes publicly accessible applications whenever possible.