Bookedited by Rune Matthiesen.
Summary: Since the publishing of the first edition, the methodologies and instrumentation involved in the field of mass spectrometry-based proteomics has improved considerably. Fully revised and expanded, Mass Spectrometry Data Analysis in Proteomics, Second Edition presents expert chapters on specific MS-based methods or data analysis strategies in proteomics. The volume covers data analysis topics relevant for quantitative proteomics, post translational modification, HX-MS, glycomics, and data exchange standards, among other topics. Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Updated and authoritative, Mass Spectrometry Data Analysis in Proteomics, Second Edition serves as a detailed guide for all researchers seeking to further our knowledge in the field of proteomics.
Contents:
Introduction to mass spectrometry-based proteomics / Rune Matthiesen and Jakob Bunkenborg
LC-MS spectra processing / Rune Matthiesen
Isotopic distributions / Alan L. Rockwood and Magnus Palmblad
Retention time prediction and protein identification / Alex A. Henneman and Magnus Palmblad
Algorithms for database-dependent search of MS/MS data / Rune Matthiesen
Interpretation of tandem mass spectra of posttranslationally modified peptides / Jakob Bunkenborg and Rune Matthiesen
Improving peptide identification using empirical scoring systems / Robert J. Chalkley
Methods and algorithms for quantitative proteomics by mass spectrometry / Rune Matthiesen and Ana Sofia Carvalho
Computational approaches to selected reaction monitoring assay design / Conrad Bessant and Jun Fan
Feature celection and machine learning with mass spectrometry data / Susmita Datta
Considerations in the analysis of hydrogen exchange mass spectrometry data / Thomas E. Wales, Michael J. Eggertson, and John R. Engen
Permethylated n-glycan analysis with mass spectrometry / Zhenxin Lin and David M. Lubman
Mass spectrometry methods for studying glycosylation in cancer / Hugo Osorio and Celso A. Reis
Proteomics data exchange and storage : the need for common standards and public repositories / Rafael C. Jimenez and Juan Antonio Vizcaıno
Tools for protein posttranslational modifications analysis : FAK, a case study / Catarina Fonseca [and others]
Proteomic strategies to characterize signaling pathways / H.C. Harsha, Sneha M. Pinto, and Akhilesh Pandey
Simple proteomics data analysis in the object-oriented powershell / Yassene Mohammed and Magnus Palmblad.