Mass spectrometry data analysis in proteomics / edited by Rune Matthiesen. -- 3rd ed. -- New York : Humana Press, 2020. – (58.17 /M592 /v.2051)

Contents

Preface

Contributors

1  Introduction to Mass Spectrometry-Based Proteomics

2  LC-MS Spectra Processing

3  Isotopic Distributions

4  Retention Time Prediction and Protein Identification

5  Comparing Peptide Spectra Matches Across Search Engines

6  Calculation of False Discovery Rate for Peptide and Protein Identification

7  Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry

8  Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides

9  Solution to Dark Matter Identified by Mass-Tolerant Database Search

10  Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-Targeted Cancer Therapies

11  Mass Spectrometry-Based Characterization of Ub-and UbL-Modified Proteins

12  Targeted Proteomics as a Tool for Quantifying Urine-Based Biomarkers

13  Data Imputation in Merged Isobaric Labeling-Based Relative Quantification Datasets

14  Clustering Clinical Data in R

15  Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics

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

17  Using the Object-Oriented PowerShell for Simple Proteomics Data Analysis

18  Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data

Index