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 Appro
