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 Jesús Vázquez

7. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry

Rune Matthiesen and Ana Sofia Carvalho

Jakob Bunkenborg, and Rune Matthiesen

9. Solution to Dark Matter Identified by Mass-tolerant Database Search

Rune Matthiesen

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 Bjødstrup Palstrøm, Rune Matthiesen, and Hans Christian Beck

14. Clustering Clinical Data in R

Ana Pina, Maria Paula Macedo, and Roberto Henriques

Mathias Walzer and  Juan Antonio Vizcaíno

16. Review of Batch Effects Prevention, Diagnostics, and Correction Approaches

Jelena Cuklina, Patrick G. A. Pedrioli, and Ruedi Aebersold

Yassene Mohammed and Magnus Palmblad

18. Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data