Microbial Proteomics: Methods and Protocols

Description

This detailed volume explores state-of-the-art methods for the identification, quantification, and characterization of microbial proteins. Split into five parts, the content addresses global sample preparation and protein enrichment, subcellular fractionation, protein quantification, analysis of post-translational protein modifications, as well as metaproteomics, a relatively new branch of microbial proteomics that investigates the proteins of all microbes comprising an environmental consortium. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Microbial Proteomics: Methods and Protocols serves as a valuable and stimulating source for all beginners and advanced researchers in the field of microbial proteomics and beyond. Chapter 18 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. Front Matter ....Pages i-xv Front Matter ....Pages 1-1 Filter-Aided Sample Preparation for Proteome Analysis (Jacek R. Wiśniewski)....Pages 3-10 Protein Enrichment from Highly Dilute Samples with StrataClean (Florian Bonn, Andreas Otto)....Pages 11-18 Front Matter ....Pages 19-19 Membrane Proteomics in Gram-Positive Bacteria: Two Complementary Approaches to Target the Hydrophobic Species of Proteins (Susanne Sievers)....Pages 21-33 Enrichment of Cell Surface-Associated Proteins in Gram-Positive Bacteria by Biotinylation or Trypsin Shaving for Mass Spectrometry Analysis (Florian Bonn, Sandra Maaß, Jan Maarten van Dijl)....Pages 35-43 Preparation of Bacterial Magnetosomes for Proteome Analysis (Oliver Raschdorf, Dirk Schüler, René Uebe)....Pages 45-57 Analysis of Legionella Metabolism by Pathogen Vacuole Proteomics (Christian Manske, Ivo Finsel, Christine Hoffmann, Hubert Hilbi)....Pages 59-76 Front Matter ....Pages 77-77 Detection and Identification of Low-Abundant Proteins Using HPE Gels, Fluorescent Stains, and MALDI-ToF-ToF-MS (Martin Moche, Dirk Albrecht, Reiner Westermeier, Knut Büttner)....Pages 79-93 Applications of Difference Gel Electrophoresis (DIGE) in the Study of Microorganisms (Kathleen Trautwein, Ralf Rabus)....Pages 95-112 Proteomic Signatures in Staphylococcus aureus (Susanne Engelmann, Stephan Fuchs)....Pages 113-130 How to Assess Protein Stability: Half-Life Determination of a Regulatory Protein in Bacillus subtilis (Alexander Reder, Stephan Michalik, Ulf Gerth)....Pages 131-140 Absolute Protein Quantification Using AQUA-Calibrated 2D-PAGE (Sandra Maaß)....Pages 141-162 Sulfur-34S and 36S Stable Isotope Labeling of Amino Acids for Quantification (SULAQ34/36) of Proteome Analyses (Florian-Alexander Herbst, Nico Jehmlich, Martin von Bergen, Frank Schmidt)....Pages 163-174 Metabolic Labeling of Microorganisms with Stable Heavy Nitrogen Isotopes (15N) (Andreas Otto)....Pages 175-188 Next-Generation Trapping of Protease Substrates by Label-Free Proteomics (Claudia Lindemann, Nikolas Thomanek, Katja Kuhlmann, Helmut E. Meyer, Katrin Marcus, Franz Narberhaus)....Pages 189-206 In vivo Proteomics Approaches for the Analysis of Bacterial Adaptation Reactions in Host–Pathogen Settings (Henrike Pförtner, Maren Depke, Kristin Surmann, Frank Schmidt, Uwe Völker)....Pages 207-228 Front Matter ....Pages 229-229 Phosphopeptide Enrichment from Bacterial Samples Utilizing Titanium Oxide Affinity Chromatography (Boumediene Soufi, Christoph Täumer, Maja Semanjski, Boris Macek)....Pages 231-247 Phosphoproteomics in Microbiology: Protocols for Studying Streptomyces coelicolor Differentiation (Angel Manteca, Beatriz Rioseras, Adelina Rogowska-Wrzesinska, Ole N. Jensen)....Pages 249-260 Thiol-Redox Proteomics to Study Reversible Protein Thiol Oxidations in Bacteria (Martina Rossius, Falko Hochgräfe, Haike Antelmann)....Pages 261-275 Front Matter ....Pages 277-277 Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host–Microbiota Interactions (Pranjul Shah, Emilie E. L. Muller, Laura A. Lebrun, Linda Wampach, Paul Wilmes)....Pages 279-291 Utilization of a Detergent-Based Method for Direct Microbial Cellular Lysis/Proteome Extraction from Soil Samples for Metaproteomics Studies (Karuna Chourey, Robert L. Hettich)....Pages 293-302 Sample Preparation for Metaproteome Analyses of Soil and Leaf Litter (Katharina M. Keiblinger, Katharina Riedel)....Pages 303-318 Centrifugation-Based Enrichment of Bacterial Cell Populations for Metaproteomic Studies on Bacteria–Invertebrate Symbioses (Tjorven Hinzke, Manuel Kleiner, Stephanie Markert)....Pages 319-334 Correction to: Thiol-Redox Proteomics to Study Reversible Protein Thiol Oxidations in Bacteria (Martina Rossius, Falko Hochgräfe, Haike Antelmann)....Pages E1-E1 Back Matter ....Pages 335-344