Part I: Sample Collection

1. Biological Sample Collection For Clinical Proteomics - Existing SOPs

Vasiliki Lygirou, Manousos Makridakis, and Antonia Vlahou

2. Targeting The Proteome Of Cellular Fractions: Focus on Secretome

Agnieszka Latosinska, Maria Frantzi, William Mullen, Antonia Vlahou and Manousos Makridakis

3. Preparation Of Urinary Exosomes: Methodological Issues For Clinical Proteomics

Marina Pitto, Samuele Corbetta, and Francesca Raimondo

4. Sample Treatment Methods Involving Combinatorial Peptide Ligand Libraries For Improved Proteomes Analyses

Pier Giorgio Righetti and Egisto Boschetti

5. Glycoprotein Enrichment Method Using A Selective Magnetic Nano-Probe Platform (MNP) Functionalized With Lectins

Marta Cova, Rui Oliveira-Silva, Jos Alexandre Ferreira, Rita Ferreira, Francisco Amado, Ana Lusa Daniel-Da-Silva, and Rui Vitorino

Part II: Technologies For Discovery and Validation

6. The Latest Advancements In Proteomic Two-Dimensional Gel Electrophoresis Analysis Applied To Biological Samples

Laura Santucci, Maurizio Bruschi, Gian Marco Ghiggeri, and Giovanni Candiano

7. 2DE Maps In The Discovery Of Human Autoimmune Kidney Diseases: The Case of Membranous Glomerulonephritis

Maurizio Bruschi, Laura Santucci, Gian Marco Ghiggeri, and Giovanni Candiano

8. MALDI-Imaging Mass Spectrometry on Tissues

Veronica Mainini, Maciej Lalowski, Athanasios Gotsopoulos, Vasiliki Bitsika, Marc Baumann, and Fulvio Magni

9. Laser Capture Microdissection Of Fluorescently Labeled Amyloid Plaques From Alzheimer's Disease Brain Tissue For Mass Spectrometric Analysis

Diana A.T. Nijholt, Christoph Stingl, and Theo M. Luider

10. Urine Sample Preparation And Fractionation For Global Proteome Profiling By LC-MS

Magali Court, Jrme Garin, and Christophe D. Masselon

11. Methods In Capillary Electrophoresis Coupled To Mass Spectrometry For The Identification Of Clinical Proteomic/Peptidomic Biomarkers In Biofluids

Angelique Stalmach, Holger Husi, Khedidja Mosbahi, Amaya Albalat, William Mullen, and Harald Mischak

12. Quantification Of Proteins In Urine Samples Using Targeted Mass Spectrometry Methods

Nina Khristenko and Bruno Domon

Part III: Extracting Biological Relevant Biomarkers and Proceeding With Implementation

13. Statistical Issues In The Design And Planning Of Proteomic Profiling Experiments

David A. Cairns

14. Integrating Proteomics Profiling Data Sets - A Network Perspective

Akshay Bhat, Mohammed Dakna, and Harald Mischak

15. The European Medicines Agency Experience With Biomarker Qualification

Efthymios Manolis, Armin Koch, Dieter Deforce, and Spiros Vamvakas