Sample Preparation in Biological Mass Spectrometry

Front Matter....Pages i-xxix
Front Matter....Pages 1-1
Gel-Based and Gel-Free Sample Preparation for LC-MS/MS Analysis....Pages 3-17
Manipulating the Mass Spectrometric Properties of Peptides through Selective Chemical Modification....Pages 19-40
Sample Preparation for 2D Electrophoresis and CE-Based Proteomics....Pages 41-60
Filtration as a Sample Preparation Technique Prior to Mass Spectrometry: Selecting the Right Filtration Device....Pages 61-75
Pressure-Assisted Lysis of Mammalian Cell Cultures Prior to Proteomic Analysis....Pages 77-90
Multiplexed Preparation of Biological Samples for Mass Spectrometry Using Gel Electrophoresis....Pages 91-105
Front Matter....Pages 107-107
Development of an On-Bead Digestion Procedure for Immunoprecipitated Proteins....Pages 109-124
Ultra-Fast Sample Preparation for High-Throughput Proteomics....Pages 125-139
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....Pages 141-155
Front Matter....Pages 157-157
Sample Preparation of Formalin-Fixed Paraffin-Embedded (FFPE) Tissue for Proteomic Analyses....Pages 159-170
Brain Proteomics: Sample Preparation Techniques for the Analysis of Rat Brain Samples Using Mass Spectrometry....Pages 171-195
Subcellular Fractionation Using Step-Wise Density Extraction for Mass Spectrometry Analysis....Pages 197-214
Front Matter....Pages 215-215
Two-Dimensional Polyacrylamide Gel Electrophoresis....Pages 217-242
Quantitative Intact Proteomic Strategies to Detect Changes in Protein Modification and Genomic Variation....Pages 243-253
Two-Dimensional Non-denaturing Gel Electrophoresis for Characterization of Proteins in Multi-molecular Particles by Mass Spectrometry....Pages 255-266
Front Matter....Pages 267-267
Preanalytical Variables for Plasma and Serum Proteome Analyses....Pages 269-289
Biomarker Discovery in Biological Fluids....Pages 291-326
Sample Handling of Body Fluids for Proteomics....Pages 327-360
Front Matter....Pages 361-361
Quantitative Plant Proteomics Using Hydroponic Isotope Labeling of Entire Plants (HILEP)....Pages 363-380
Efficient Strategies for Analysis of Low Abundance Proteins in Plant Proteomics....Pages 381-409
Front Matter....Pages 361-361
Plant Plasma Membrane Proteomics: Challenges and Possibilities....Pages 411-434
Front Matter....Pages 435-435
Affinity and Chemical Enrichment for Mass Spectrometry-Based Proteomics Analyses....Pages 437-486
A Multidimensional Chromatography Strategy Using HILIC and IMAC for Quantitative Phosphoproteome Analysis....Pages 487-495
Glycomic Analysis of Membrane-Associated Proteins....Pages 497-513
Multi-lectin Affinity Chromatography (M-LAC) Combined with Abundant Protein Depletion for Analysis of Human Plasma in Clinical Proteomics Applications....Pages 515-534
Analysis of Glycopeptides Using Porous Graphite Chromatography and LTQ Orbitrap XL ETD Hybrid MS....Pages 535-546
Front Matter....Pages 547-547
Stable Isotopic Labeling for Proteomics....Pages 549-573
Standard Operating Procedures and Protocols for the Preparation and Analysis of Plasma Samples Using the iTRAQ Methodology....Pages 575-624
Front Matter....Pages 625-625
Methods for the Isolation of Phosphoproteins and Phosphopeptides for Mass Spectrometry Analysis: Toward Increased Functional Phosphoproteomics....Pages 627-655
Adipose Tissue Lysis and Protein Extraction Followed by MS-based Proteomic Profiling Reveals Constituents of Oxidative Stress in Obesity....Pages 657-670
Protocols for LC-MS/MS-Based Quantitative Analysis of Proteolytic Substrates from Complex Mixtures....Pages 671-687
Front Matter....Pages 689-689
Mass Spectrometry-Based Proteomics Analyses of Integral Membrane Proteins....Pages 691-714
Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry of Hydrophobic Proteins in Mixtures....Pages 715-729
Front Matter....Pages 731-731
MALDI MS-Based Biomarker Profiling of Blood Samples....Pages 733-747
Sample Preparation in Biological Analysis by Atmospheric Pressure Matrix Assisted Laser/Desorption Ionization (AP-MALDI) Mass Spectrometry....Pages 749-764
MALDI Imaging Mass Spectrometry for Investigating the Brain....Pages 765-783
UV MALDI for DNA Analysis and the Developments in Sample Preparation Methods....Pages 785-810
Front Matter....Pages 811-811
Sample Preparation Techniques for Cancer Proteomics....Pages 813-828
Sample Preparation of Primary Astrocyte Cellular and Released Proteins for 2-D Gel Electrophoresis and Protein Identification by Mass Spectrometry....Pages 829-849
Front Matter....Pages 851-851
Mass Spectrometry-Based Metabolomics. Sample Preparation, Data Analysis, and Related Analytical Approaches....Pages 853-868
Front Matter....Pages 851-851
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)....Pages 869-875
Quantitative Analysis of Lipid Peroxidation Products Using Mass Spectrometry....Pages 877-884
Sample Preparation for Drug Metabolism Studies....Pages 885-909
Front Matter....Pages 911-911
Development of Micro-scale Sample Preparation and Prefractionation Methods in LC-MS-Based Proteomic Studies....Pages 913-924
Revisiting Jurassic Park: The Isolation of Proteins from Amber Encapsulated Organisms Millions of Years Old....Pages 925-938
Front Matter....Pages 939-939
Inactivation and Extraction of Bacterial Spores for Systems Biological Analysis....Pages 941-977
Front Matter....Pages 979-979
New Developments in LC-MS and Other Hyphenated Techniques....Pages 981-1030
Reversed-Phase HPLC of Peptides – A Valuable Sample Preparation Tool in Bottom-Up Proteomics: Separation Selectivity in Single and Multi-dimensional Separation Modes....Pages 1031-1050
Applications of Microfluidic Devices with Mass Spectrometry Detection in Proteomics....Pages 1051-1074
Back Matter....Pages 1075-1089