Sample Preparation in Biological Mass Spectrometry (eBook)

Introduction: Sample Preparation – Boring but Important! Alexander Lazarev1 and Alexander R. Ivanov Section I. Traditional and improved techniques in sample preparation for proteomics 1. Gel-based and Gel-free Sample Preparation for LC-MS/MS Analysis; Xianyin Lai and Frank A. Witzmann 2. Manipulating the Mass Spectrometric Properties of Peptides through Selective Chemical Modification; David Arnott, Peter S. Liu, Patricia Molina, Lilian Phu, and Wendy N. Sandoval 3. Sample Preparation for 2D Electrophoresis and CE-based Proteomics; Judit M. Nagy, Alexandria Lipka, Fiona Pereira, Nicky Marlin, and Stuart Hassard 4. Filtration as a Sample Preparation Technique Prior to Mass Spectrometry: Selecting the Right Filtration Device; Vivek Joshi and Elena Chernokalskaya 5. Pressure-Assisted Lysis of Mammalian Cell Cultures Prior to Proteomic Analysis; Emily Freeman, Yelena Margolin, and Alexander R. Ivanov 6. Multiplexed Preparation of Biological Samples for Mass Spectrometry using Gel Electrophoresis; Jeremy L. Norris, Alan A. Doucette Section II. Methods for Improved Proteolytic Digestion 7. Development of an On-bead Digestion Procedure for Immunoprecipitated Proteins; Matthew J. Berberich, Jeffrey Kowalak, Anthony Makusky, Brian Martin, Detlef Vullhorst, Andres Buonanno, and Sanford Markey 8. Ultra-Fast Sample Preparation for High-Throughput Proteomics; Daniel Lopez-Ferrer, Kim K. Hixson, Mikhail E. Belov, and Richard D. Smith 9. Exploring the Capabilities of the Protein Identification by Unconventional Sample Preparation Approaches: LC/MALDI/On-target Digestion Approach and High Pressure-assisted In-gel Tryptic Digestion; Melkamu Getie-Kebtie and Michail A. Alterman Section III. Methods for Tissue, Cell, and Organelle Preparation and Analysis 10. Sample Preparation of Formalin-Fixed Paraffin-Embedded (FFPE) Tissue for Proteomic Analyses; Diem Tran, Mark Daniels, Ben Colson, Dikran Aivazian, Antonio Boccia, Ingrid Joseph, Steffan Ho, Steve French, Alex Buko, and Jing Wei 11. Brain Proteomics: Sample Preparation Techniques for the Analysis of Rat Brain Samples using Mass Spectrometry; Yoshinori Masuo, Misato Hirano, Junko Shibato, Hyung Wook Nam, Isabelle Fournier, Mériaux Céline, Maxence Wisztorski, Michel Salzet, Hideaki Soya, Ganesh Kumar Agrawal, and Randeep Rakwal 12. Subcellular Fractionation Using Step-Wise Density Extraction for Mass Spectrometry Analysis; WenKui Lan, Marc J. Horn, Fumihiko Urano, Andre Kopoyan, and Sun W. Tam Section IV. 2D Gel-based Proteomics 13. Two-dimensional Polyacrylamide Gel Electrophoresis; Aisling A. Robinson, Ciara A. McManus, and Michael J. Dunn 14. Quantitative Intact Proteomic Strategies to Detect Changes in Protein Modification and Genomic Variation; David B. Friedman 15. Two-dimensional Non-denaturing Gel Electrophoresis for Characterization of Proteins in Multi-molecular Particles by Mass Spectrometry; Susan T. Weintraub and Philip Serwer Section V. Sample Preparation and Analysis Techniques for Biological Fluids and Biomarker Discovery 16. Pre-Analytical Variables for Plasma and Serum Proteome Analyses; Craig A. Gelfand and Gilbert S. Omenn 17. Biomarker Discovery in Biological Fluids; Wasfi Alrawashdeh and Tatjana Crnogorac-Jurcevic 18. Sample Handling of Body Fluids for Proteomics; Joao A. Paulo, Ali R. Vaezzadeh, Darwin L. Conwell, Richard S. Lee, and Hanno Steen Section VI. Sample Preparation Methods in Plant Proteomics 19. Quantitative Plant Proteomics Using Hydroponic Isotope Labeling of Entire Plants (HILEP); Laurence V. Bindschedler, Celia J. Smith and Rainer Cramer 20. Efficient Strategies for Analysis of Low Abundance Proteins in Plant Proteomics; Olga A. Koroleva, Laurence V. Bindschedler 21. Plant Plasma Membrane Proteomics: Challenges and Possibilities; Anders Laurell Blom Møller, Katja Witzel, Annelies Vertommen, Vibeke Barkholt, Birte Svensson, Sebastien Carpentier, Hans-Peter Mock, and Christine Finnie Section VII. Affinity Interaction and Biochemichal Enrichment Techniques 22. Affinity and Chemical Enrichment for Mass Spectrometry-based Proteomics Analyses; Guillaume Adelmant, Job D. Cardoza, Scott B. Ficarro, Timothy W. Sikorski, Yi Zhang, and Jarrod A. Marto 23. A Multidimensional Chromatography Strategy using HILIC and IMAC for Quantitative Phosphoproteome Analysis; Dean E. McNulty, Michael J. Huddleston, and Roland S. Annan 24. Glycomic Analysis of Membrane Associated Proteins; Diarmuid T. Kenny, Liaqat Ali, Samah Issa, and Niclas G. Karlsson 25. Multi-Lectin Affinity Chromatography (M-LAC) in combination with High Abundance Protein Depletion for the Discovery of Glycoprotein Disease Biomarkers; Marina Hincapie, Tatiana Plavina, William S. Hancock 26. Analysis of Glycopeptides Using Porous Graphite Chromatography and LTQ Orbitrap XL ETD Hybrid MS; Terry Zhang, Rosa Viner, Zhiqi Hao, Vlad Zabrouskov Section VIII. Methods for Quantitative proteomics 27. Stable Isotopic Labeling for Proteomics; Keith Ashman, María Isabel Ruppen Cañás, Jose L. Luque-Garcia, and Fernando García Martínez 28. Standard Operating Procedures and Protocols for the Preparation and Analysis of Plasma Samples Using the iTRAQ Methodology; Leanne B. Ohlund, Darryl B. Hardie, Monica H. Elliott, Derek S. Smith, Jennifer D. Reid, Gabriela V. Cohen-Freue, Axel P. Bergman, Mayu Sasaki, Lisa Robertson, Robert F. Balshaw, Raymond T. Ng, Alice Mui, Bruce M. McManus, Paul A. Keown, W. Robert McMaster, Carol E. Parker, and Christoph H. BorchersSection IX. Sample Preparation in Functional Proteomics 29. Methods for the Isolation of Phosphoproteins and Phosphopeptides for Mass Spectrometry Analysis: Toward Increased Functional Phosphoproteomics; Tapasree Goswami and Bryan A. Ballif 30. Adipose Tissue Lysis and Protein Extraction Followed by MS-based Proteomic Profiling Reveals Constituents of Oxidative Stress in Obesity; Emily A Freeman, Vera Gross, Ilyana Romanovsky, Alexander Lazarev, and Alexander R Ivanov 31. Protocols for LC-MS/MS-based Quantitative Analysis of Proteolytic Substrates from Complex Mixtures ; Mari Enoksson, Miklós Békés, Laurence M. Brill, and Khatereh Motamedchaboki Section X. Characterization of Membrane Proteins 32. Mass Spectrometry-based Proteomics Analyses of Integral Membrane Proteins ; Eric Bonneil, Sylvain Brunet, Michel Jaquinod, Joseph P.M. Hui, Anik Forest, and Pierre Thibault 33. Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry of Hydrophobic Proteins in Mixtures; Rachel R. Ogorzalek Loo Section XI. Methods for MALDI MS Enabled Biomedical Applications 34. MALDI MS-based Biomarker Profiling of Blood Samples; Ali Tiss, Celia J. Smith, and Rainer Cramer 35. Sample Preparation in Biological Analysis by Atmospheric Pressure Matrix Assisted Laser/Desorption Ionization (AP-MALDI) Mass Spectrometry; Appavu K. Sundaram, Berk Oktem, Jane Razumovskaya, Shelley N. Jackson, Amina S. Woods, and Vladimir M. Doroshenko 36. MALDI Imaging Mass Spectrometry for Investigating the Brain; Isabelle Fournier, Mériaux Céline, Maxence Wisztorski, Randeep Rakwal and Michel Salzet 37. UV MALDI for DNA Analysis and the Developments in Sample Preparation Methods; Igor P. Smirnov Section XII. Clinical Research and Applications 38. Sample Preparation Techniques for Cancer Proteomics; Paul Dowling, Martin Clynes, and Dr. Paula Meleady 39. Sample Preparation of Primary Astrocyte Cellular and Secreted Proteins for 2-D Gel Electrophoresis and Protein Identification by Mass Spectrometry; Melissa A. Sondej, Philip Doran, Joseph A. Loo, and Ina-Beate Wanner Section XIII. Sample Preparation Techniques in Metabolomics and Drug Discovery 40. Mass Spectrometry-based Metabolomics. Sample Preparation, Data Analysis, and Related Analytical Approaches; Oliver A.H. Jones, Lee D. Roberts, and Mahon L. Maguire 41. Targeted Quantitative Analysis of Jasmonic Acid (JA) and its Amino Acid Conjugates in Plant Using HPLC-Electrospray Ionization-Tandem Mass Spectrometry (ESI-LC-MS/MS); Shigeru Tamogami, Ganesh Kumar Agrawal, and Randeep Rakwal 42. Quantitative Analysis of Lipid Peroxidation Products using Mass Spectrometry; Yasukazu Yoshida and Mototada Shichiri 43. Samples preparation for drug metabolism studies; Natalia Penner, Biplab Das, Caroline Woodward, and Chandra Prakash Section XIV. Sample Preparation in Analysis or Exotic and Limited Availability Specimens 44. Development of Micro-scale Sample Preparation and Prefractionation Methods in Shotgun Proteomic Studies; Lan Dai, Chen Li, and David M Lubman 45. Revisiting Jurassic Park: The Isolation of Proteins from Aamber Encapsulated Organisms Millions of Years Old; Gary B. Smejkal, George O. Poinar Jr., Pier Giorgio Righetti, and Feixia Chu Section XV. Sample Treatment in Biodefense, Forensics and Infectious Diseases 46. Inactivation and Extraction of Bacterial Spores for Systems Biological Analysis; Bradford S. Powell and Robert J. Cybulski Section XVI. Novel Approaches in Sample Preparation and LC-MS Analysis 47. New Developments in LC-MS and Other Hyphenated Techniques; Mikhail Belov, Ruwan Kurulugama, Daniel Lopez-Ferrer, Yehia Ibrahim, Erin Baker 48. Reversed-phase HPLC of Peptides – a Valuable Sample Preparation Tool in Bottom-up Proteomics: Separation Selectivity in Single and Multi-dimensional Separation Modes; Ravi C. Dwivedi, Vic Spicer, Oleg V. Krokhin 49. Applications of Microfluidic Devices with Mass Spectrometry Detection in Proteomics; Xiuli Mao and Iulia M. Lazar