The Low Molecular Weight Proteome Methods and Protocols

About this book

Small proteins with molecular weights of <25 kDa are involved in major biological processes such as ribosome formation, stress adaption and cell cycle control. The study of the low-molecular-weight proteome has identified many central regulators of biology such as cytokines, chemokines, peptide hormones and proteolytic fragments of larger proteins. Due to the unique features of these proteins, the technical challenges are different from those in "common" proteomics.

In The Low Molecular Weight Proteome: Methods and Protocols expert researchers from the field provide protocols for analysis of low molecular weight proteins and peptides, protocols for such methods applied in clinical research and an up-to-date review of quantitative protein profiling by labeling. These include methods suitable for both peptide and protein analysis with focus on methods and application that can be used for small protein analysis.

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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, The Low Molecular Weight Proteome: Methods and Protocols is a useful resource for experienced proteomics practitioners as well as an aid to newcomers who wish to become acquainted with the theory and practice of a wide array of methods in analyzing small proteins or peptides.

Contents

Part I: Low Molecular Weight Analysis Methods
1. Narrow Range Peptide Iso Electric Focusing as Peptide Prefractionation Method Prior to Tandem Mass Spectrometry Analysis Maria Pernemalm
2. Analysis of Peptides by Denaturing Ultrafiltration and LC-MALDI-TOF-MS Yanming An and Radoslav Goldman
3. Stable Isotope Labeling Methods in Protein Profiling Johan Lengqvist and AnnSofi Sandberg
4. Development of MRM-based Assays for the Absolute Quantitation of Plasma Proteins Michael A. Kuzyk, Carol E. Parker, Dominik Domanski, and Christoph H. Borchers
5. Mass Spectrometric Profiling of Low-Molecular-Weight Proteins Matthias Rainer, Constantin Sajdik, and Gunther K. Bonn
6. Developing an iMALDI Method Brinda Shah, Jennifer D. Reid, Michael A. Kuzyk, Carol E. Parker, and Christoph H. Borchers
7. Analysis of Neuropeptides by MALDI Imaging Mass Spectrometry Anna Karlsson, Jorg Hanrieder, Jonas Bergquist, and Malin Andersson
8. Highly Multiplexted Antibody Suspension Bead Arrays for Plasma Protein Profiling By Kimi Drobin, Peter Nilsson and Jochen M. Schwenk

Part II: Bioinformatics of Proteomics Data
9. Protein Quantification by Peptide Quality Control (PQPQ) of Shotgun Proteomics Data Jenny Forshed
10. Collection and Handling of Blood Specimens for Peptidomics Harald Tammen and Rudiger Hess

Part III: Methods Applied in Clinical Research
11. An Automated RP-SCX Solid Phase Extraction Procedure for Urinary Peptidomics Biomarker Discovery Studies Crina I.A. Balog, Rico Derks, Oleg A. Mayboroda and Andre M. Deelder
12. Application of Phage Display for Ligand Peptidomics to Identify Peptide Ligands Binding to AQP2-expressing Membrane Fractions Byung-Heon Lee and Tae-Hwan Kwon
13. Protein Expression Profiling of Brain Tumor Tissue Using SELDI-MS Carl Wibom
14. Comprehensive Analysis of MHC Ligands in Clinical Material by Immunoaffinity - Mass Spectrometry Kie Kasuga

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