Introduction to Proteomics / Rune Matthiesen and Kudzai E. Mutenda -- Extracting Monisotopic Single-Charge Peaks From Liquid Chromatography-Electrospray Ionization-Mass Spectrometry / Rune Matthiesen -- Calibration of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Peptide Mass Fingerprinting Spectra / Karin Hjernø and Peter Højrup -- Protein Identification by Peptide Mass Fingerprinting / Karin Hjernø -- Generating Unigene Collections of Expressed Sequence Tag Sequences for Use in Mass Spectrometry Identification / Jeppe Emmersen -- Protein Identification by Tandem Mass Spectrometry and Sequence Database Searching / Alexey I. Nesvizhskii -- Virtual Expert Mass Spectrometrist v3.0: An Integrated Tool for Proteome Analysis / Rune Matthiesen -- Quantitation With Virtual Expert Mass Spectrometrist / Albrecht Gruhler and Rune Matthiesen -- Sequence Handling by Sequence Analysis Toolbox v1.0 / Christian Ravnsborg Ingrell, Rune Matthiesen, and Ole Nørregaard Jensen -- Interpretation of Collision- Induced Fragmentation Tandem Mass Spectra of Posttranslationally Modified Peptides / Jakob Bunkenborg and Rune Matthiesen -- Retention Time Prediction and Protein Identification / Magnus Palmblad -- Quantitative Proteomics by Stable Isotope Labeling and Mass Spectrometry / Sheng Pan and Ruedi Aebersold -- Quantitative Proteomics for Two-Dimensional Gels Using Difference Gel Electrophoresis / David B. Friedman -- Proteomic Data Exchange and Storage: The Need for Common Standards and Public Repositories / Sandra Orchard ... [et al.] -- Organization of Proteomics Data With YassDB / Allan L. Thomsen ... [et al.] -- Analysis of Carbohydrates by Mass Spectrometry / Kudzai E. Mutenda and Rune Matthiesen -- Useful Mass Spectrometry Programs Freely Available on the Internet / Rune Matthiesen -- Index