Quantitative Proteomics by Mass Spectrometry

ISBN-13: 9781493935222 / Angielski / Twarda / 2016 / 306 str.

Salvatore Sechi

Opis

This volume describes prominent methodologies developed by laboratories that have been leading the field of quantitative proteomics by mass spectrometry. The procedures for performing the experiments are described in an easy-to-understand manner with many technical details that usually are not reported in typical research articles. This second edition of Quantitative Proteomics by Mass Spectrometry provides a broad perspective of the methodologies used for quantifying proteins and post-translational modifications in different types of biomedical specimens. 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 thorough, Quantitative Proteomics by Mass Spectrometry, Second Edition is a valuable resource to help researchers understand and learn about the latest tools used in the study of quantitative proteomics by mass spectrometry.

Spis treści

1. Increased Depth and Breadth of Plasma Protein Quantitation via Two Dimensional Liquid Chromatography/Multiple Reaction Monitoring-Mass Spectrometry with Labeled Peptide Standards
Andrew J. Percy, Juncong Yang, Andrew G. Chambers, and Christoph H. Borchers

2. Quantitative Analysis of the Wirt5-Regulated Lysine Succinylation Proteome in Mammalian Cells
Yue Chen

3.      Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy
Todd M. Greco, Amanda J. Guise, and Ileana M. Cristea

4.      Label-Free Quantitation for Clinical Proteomics
Robert Moulder, Young Ah Goo, and David R. Goodlett

5.      Proteogenomic Methods to Improve Genome Annotation
Keshava K. Datta, Anil K. Madugundu, and Harsha Gowda

6.  Mass Spectrometry-Based Quantitative O-GlcNAcomic Analysis
Junfeng Ma and Gerald W. Hart

7.      Isolating and Quantifying Plasma HDL Proteins by Sequential Density Gradient Ultracentrifugation and Targeted Proteomics
Clark M. Henderson, Tomas Vaisar, and Andrew N. Hoofnagle

8.      A Method for Label-Free Differential Top-Down Proteomics
Ioanna Ntai, Timothy K. Toby, Richard D. LeDuc, and Neil L. Kelleher

9.      Multiplexed Immunoaffinity Enrichment of Peptides with Anti-Peptide Antibodies and Quantification by Stable Isotope Dilution Multiple Reaction Monitoring Mass Spectrometry
Eric Kuhn and Steven A. Carr

10.   High Throughput Quantitative Proteomics Enabled by Mass Defect-Based 12-Plex DiLeu Isobaric Tags
Dustin C. Frost and Lingjun Li

11.   Isotopic N, N-Dimethyl Leucine (iDiLeu) for Absolute Quantification of Peptides Using a Standard Curve Approach
Tyler Greer and Lingjun Li

12.   Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards
James G. Bollinger, Andrew B. Stergachis, Richard S. Johnson, Jarrett D. Egertson, and Michael J. MacCoss

13.   Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays
Jeffrey R Whiteaker, Goran N. Halusa, Andrew N. Hoofnagle, Vagisha Sharma, Brendan MacLean, Ping Yan, John A. Wrobel, Jacob Kennedy, DR Mani, Lisa J. Zimmerman, Matthew R. Meyer, Mehdi Mesri, Susan E. Abbatiello, Emily Boja, Stven A. Carr, Daniel W. Chan, Xian Chen, Jing Chen, Sherri R. Davies, Matthew J. C. Ellis, David Fenyö, Tara Hiltke, Karen A. Ketchum, Chris Kinsinger, Eric Kuhn, Daniel C. Liebler, De Lin, Tao Liu, Michael Loss, Michael J. MacCoss, Wei-Jun Qian, Robert Rivers, Karin D. Rodland, Kelly V. Ruggles, Mitchell G. Scott, Richard D. Smith, Stefani Thomas, R. Reid Townsend, Gordon Whiteley, Chaochao Wu, Hui Zhang, Zhen Zhang, Henry Rodriguez, and Amanda G. Paulovich

14.   Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Lableing Coupled with Two-Dimensional LC-MS/MS
Marina A. Gritsenko, Zhe Xu, Tao Liu, and Richard D. Smith

15.   Multiple and Selective Reaction Monitoring Using Triple Quadrupole Mass Spectrometer: Pre-Clinical Large Cohort Analysis
Qin Fu, Zhaohui Chen, Shenyan Zhang, Sarah Parker, Zongming Fu, Xiaoqian  Liu, Josef Coresh, and Jennifer E. Van Eyk

16.   Methods for SWATH™: Data Independent Acquisition on TripleTOF Mass Spectrometers
Ronald J. Holewinski, Sarah J. Parker, Andrea D. Matlock, Vidya Venkatraman, and Jennifer E. Van Eyk

17.   Measurement of Phosphorylated Peptides with Absolute Quantification
Raven J. Reddy, Timothy G. Curran, Yi Zhang, and Forest M. White

18.      Proteomic Analysis of Protein Turnover by Metabolic Whole Rodent Pulse-Chase Isotopic Labeling and Shotgun Mass Spectrometry Analysis

Jeffrey N. Savas, Sung Kyu Park, and John R. Yates III