Mass Spectrometry Data Analysis in Proteomics

1. Introduction to Mass Spectrometry-based Proteomics Rune Matthiesen and Jakob Bunkenborg 2. LC-MS Spectra Processing Rune Matthiesen 3. Isotopic Distributions Alan L. Rockwood and Magnus Palmblad 4. Retention Time Prediction and Protein Identification Alex Henneman and Magnus Palmblad 5. Comparing Peptide Spectra Matches Across Search Engines Rune Matthiesen, Gorka Prieto and Hans Christian Beck 6. Calculation of False Discovery Rate for Peptide and Protein Identification Gorka Prieto and Jesus Vazquez 7. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry Rune Matthiesen and Ana Sofia Carvalho 8. Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides Jakob Bunkenborg, and Rune Matthiesen 9. Solution to Dark Matter Identified by Mass-tolerant Database Search Rune Matthiesen 10. Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-targeted Cancer Therapies Barnali Deb, Irene A. George, Jyoti Sharma, and Prashant Kumar 11. Mass Spectrometry Based Characterization of Ub- and UbL-modified Proteins Nagore Elu, Benoit Lectez, Juanma Ramirez, Nerea Osinalde, and Ugo Mayor 12. Targeted Proteomics as a Tool for Quantifying Urine-based Biomarkers Sonali V Mohan, David S Nayakanti, Gajanan Sathe, Irene A Geroge, Harsha Gowda, PrashantKumar 13. Data Imputation in Merged Isobaric Labelling-based Relative Quantification Datasets Nicolai Bjodstrup Palstrom, Rune Matthiesen, and Hans Christian Beck 14. Clustering Clinical Data in R Ana Pina, Maria Paula Macedo, and Roberto Henriques 15. Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics Mathias Walzer and Juan Antonio Vizcaino 16. Review of Batch Effects Prevention, Diagnostics, and Correction Approaches Jelena Cuklina, Patrick G. A. Pedrioli, and Ruedi Aebersold 17. Using the Object-oriented PowerShell for Simple Proteomics Data Analysis Yassene Mohammed and Magnus Palmblad 18. Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data Michael J. Eggertson, Keith Fadgen,John R. Engen, and Thomas E. Wales