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Chemistry - Analytical Chemistry | Sample Preparation in Biological Mass Spectrometry

Sample Preparation in Biological Mass Spectrometry

Ivanov, Alexander R., Lazarev, Alexander V. (Eds.)

2011, XXIX, 1089p. 253 illus., 104 illus. in color.

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  • There are very few books on this topic
  • Presents examples of successful optimization and validation of sample preparation for biomedical analysis
  • Latest trends in biological analysis are well covered
  • Contains comprehensive reviews that would help the reader to acquire the most current experience in certain fields of biological sample preparation
  • Numerous step-by-step protocols help the reader to develop new applications quickly and efficiently and to avoid common problems

The goal and philosophy of sample preparation in biological mass spectrometry is to reveal the actual multicomponent molecular structure of a biological specimen that can be assessed by mass spectrometry tools. Unfortunately, sample preparation is often looked at as a necessary but “boring” step which does not warrant any efforts beyond a paragraph or two in a “Methods” section; it is believed not to be conducive to innovation, and does not elicit the enthusiasm of funding agencies. Nevertheless, in recent years, the attention to sample preparation methods has risen considerably, both in Academia and in the life science industry. The aim of this book is to provide the researcher with important sample preparation strategies for a wide variety of analyte molecules, specimens, methods, and biological applications demanding mass spectrometric analysis as the detection end-point. In this volume we have compiled contributions from several laboratories that employ mass spectrometry for biological analysis.

With the latest inventions and the introduction of highly sophisticated mass spectrometry equipment, sample preparation has become an extremely important bottleneck of biomedical analysis. This book is structured as a compilation of contributed chapters ranging from step-by-step protocols to research articles and reviews. The main philosophy of this volume is that sample preparation methods have to be optimized and validated for every project, for every sample type and for every downstream analytical technique.

Content Level » Research

Keywords » Analytical biochemistry - Mass spectrometry - Proteomics and protein chemistry - Protocols and novel techniques - Sample preparation

Related subjects » Analytical Chemistry - Biochemistry & Biophysics - Biomedical Sciences - Biophysics & Biological Physics

Table of contents 

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. Borchers

Section 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

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