This introductory proteome analysis workshop is designed to expose participants to fundamental technology platforms and current information in the field of proteomics. The course will cover bottom up quantitative and non-quantitative electrospray liquid chromatography tandem mass spectrometry (ESI-LC/MS/MS) and “multidimensional protein identification technology (Mudpit LC/LC/MS/MS)” based proteomics using complex mixtures of proteins. Participants will perform in-gel digestions, phosphopeptide enrichment, identification, and database searching using open source software such as X! Tandem and OMSSA with MS/MS data generated during the course. Lectures will cover: fundamentals of protein chemistry and mass spectrometry (MS), MS based protein identification, posttranslational modification of proteins, label free methods of protein quantitation, database searching using MS/MS data, and traditional tools of protein biochemistry. Mass spectrometry and computer lab sessions will include hands on practical applications of the techniques, using state of the art instrumentation and software. Specific course topics may change due to sample and mass spectrometer availability.