Mass Spectrometry Data Analysis in Proteomics

<p>1. Introduction to Mass Spectrometry-Based Proteomics</p><p>            Rune Matthiesen and Jakob Bunkenborg</p><p> </p><p>2. LC-MS Spectra Processing</p><p>            Rune Matthiesen</p><p> </p><p>3. Isotopic Distributions</p><p>            Alan L. Rockwood and Magnus Palmblad</p><p> </p><p>4. Retention Time Prediction and Protein Identification</p><p>            Alex A. Henneman and Magnus Palmblad</p><p> </p><p>5. Algorithms for Database Dependent Search of MSMS Data</p><p>            Rune Matthiesen</p><p> </p><p>6. Interpretation of Tandem Mass Spectra of Post-Translationally Modified Peptides</p><p>            Jakob Bunkenborg and Rune Matthiesen</p><p> </p><p>7. Improving Peptide Identification Using Empirical Scoring Systems</p><p>            Robert J. Chalkley</p><p> </p><p>8. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry</p><p>            Rune Matthiesen and Ana Sofia Carvalho</p><p> </p><p>9. Computational Approaches to Selected Reaction Monitoring (SRM) Assay Design</p><p>            Conrad Bessant and Jun Fan</p><p> </p><p>10. Feature Selection and Machine Learning with Mass Spectrometry Data</p><p>            Susmita Datta</p><p> </p><p>11. Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data</p><p>            Thomas E. Wales, Michael J. Eggertson, and John R. Engen</p><p> </p><p>12. Permethylated N-Glycan Analysis with Mass Spectrometry</p><p>            Zhenxin Lin and David M. Lubman</p><p> </p><p>13. Mass Spectrometry Methods for Studying Glycosylation in Cancer</p><p>            Hugo Osório and Celso A. Reis</p><p> </p><p>14. Proteomics Data Exchange and Storage: The Need for Common Standards and Public Repositories</p><p>            Rafael C. Jiménez and Juan Antonio Vizcaíno</p><p> </p><p>15. Tools for Protein Post Translational Modifications Analysis: FAK, A Case Study</p><p>            Catarina Fonseca, Paula Voabil, Ana Sofia Carvalho, and Rune Matthiesen</p><p> </p><p>16. Proteomic Strategies to Characterize Signaling Pathways</p><p>            H.C. Harsha, Sneha M. Pinto, and Akhilesh Pandey</p><p> </p><p>17. Simple Proteomics Data Analysis in the Object-Oriented PowerShell</p><p>            Yassene Mohammed and Magnus Palmblad</p>