Mass Spectrometry Data Analysis in Proteomics

✍ Scribed by Rune Matthiesen

• Publisher: Springer New York;Humana
• Year: 2020
• Tongue: English
• Leaves: 445
• Series: Methods in Molecular Biology 2051
• Edition: 3rd ed. 2020
• Category: Library

✦ Synopsis

The aim of this new edition is to provide detailed information on each topic and present novel ideas and views that can influence future developments in mass spectrometry-based proteomics. In contrast to the previous editions, this third edition aims to provide the most relevant computational methods, focusing on computational concepts. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Mass Spectrometry Data Analysis in Proteomics, Third Edition to ensure successful results in the further study of this vital field.

✦ Table of Contents

Front Matter ....Pages i-x
Introduction to Mass Spectrometry-Based Proteomics (Rune Matthiesen, Jakob Bunkenborg)....Pages 1-58
LC-MS Spectra Processing (Rune Matthiesen)....Pages 59-77
Isotopic Distributions (Alan L. Rockwood, Magnus Palmblad)....Pages 79-114
Retention Time Prediction and Protein Identification (Alex Henneman, Magnus Palmblad)....Pages 115-132
Comparing Peptide Spectra Matches Across Search Engines (Rune Matthiesen, Gorka Prieto, Hans Christian Beck)....Pages 133-143
Calculation of False Discovery Rate for Peptide and Protein Identification (Gorka Prieto, Jesús Vázquez)....Pages 145-159
Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry (Rune Matthiesen, Ana Sofia Carvalho)....Pages 161-197
Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides (Jakob Bunkenborg, Rune Matthiesen)....Pages 199-230
Solution to Dark Matter Identified by Mass-Tolerant Database Search (Rune Matthiesen)....Pages 231-240
Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-Targeted Cancer Therapies (Barnali Deb, Irene A. George, Jyoti Sharma, Prashant Kumar)....Pages 241-264
Mass Spectrometry-Based Characterization of Ub- and UbL-Modified Proteins (Nagore Elu, Benoit Lectez, Juanma Ramirez, Nerea Osinalde, Ugo Mayor)....Pages 265-276
Targeted Proteomics as a Tool for Quantifying Urine-Based Biomarkers (Sonali V. Mohan, D. S. Nayakanti, Gajanan Sathe, Irene A. George, Harsha Gowda, Prashant Kumar)....Pages 277-295
Data Imputation in Merged Isobaric Labeling-Based Relative Quantification Datasets (Nicolai Bjødstrup Palstrøm, Rune Matthiesen, Hans Christian Beck)....Pages 297-308
Clustering Clinical Data in R (Ana Pina, Maria Paula Macedo, Roberto Henriques)....Pages 309-343
Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics (Mathias Walzer, Juan Antonio Vizcaíno)....Pages 345-371
Review of Batch Effects Prevention, Diagnostics, and Correction Approaches (Jelena Čuklina, Patrick G. A. Pedrioli, Ruedi Aebersold)....Pages 373-387
Using the Object-Oriented PowerShell for Simple Proteomics Data Analysis (Yassene Mohammed, Magnus Palmblad)....Pages 389-405
Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data (Michael J. Eggertson, Keith Fadgen, John R. Engen, Thomas E. Wales)....Pages 407-435
Back Matter ....Pages 437-445

✦ Subjects

Chemistry; Mass Spectrometry; Proteomics