Main description:

This third volume provides comprehensive protocols on pre-analytical, analytical, plasma, and serum proteomics. New and updated chapters are divided into nine sections, detailing blood processing and handling strategies, discovery- and targeted-based mass spectrometry, including workflows to aid in discovery and targeted data analysis, in addition to software and bioinformatics for the plasma proteome. This edition further integrates emerging areas in the development of technologies for plasma proteomics and assay platforms in biomarker discovery and translational proteomics, enrichment and detection strategies to understand the plasma proteome, and peptide, lipid and metabolite targeted assays. We also detail the emerging analysis of extracellular vesicles isolated from plasma.

Written in the format of the highly successful Methods in Molecular Biology series, each of the 33 chapters includes an introduction to the topic, lists necessary materials and methods, includes hints and tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Authoritative and cutting-edge, Serum/Plasma Proteomics: Methods and Protocols, Third Edition aims to be comprehensive guide for researchers.

Contents:

Part I: Blood Processing and Handling Strategies

1 Protocols for the Isolation of Platelets for Research and Contrast to Production of Platelet Concentrates for Transfusion

2. Collection of plasma samples in areas with limited healthcare access

3. Blood Collection Processing & Handling for Plasma and Serum Proteomics

4 Preparation of cryoprecipitate and cryo-depleted plasma for proteomic research analysis

Part II: Discovery-based Mass Spectrometry

5 High throughput proteome profiling of plasma and native plasma complexes using native chromatography

6 High-throughput and in-depth proteomic profiling of 5 L plasma and serum using TMTpro 16plex

7 In depth data-independent acquisition proteomics of human plasma identifies low abundant proteins

8 In-depth Blood Proteome Profiling by Extensive Fractionation and multiplexed quantitative mass spectrometry

9 Early cancer biomarker discovery using DIA-MS proteomic analysis of EVs from peripheral blood

Part III Developments in Technologies for Plasma Proteomics

10 Strategies to enrich, identify and characterize glycoproteome in blood plasma using Liquid Chromatography High Resolution Mass Spectrometry

11 Proteome analysis of whole blood collected by volumetric absorptive microsampling

12 Proteomic applications and considerations: from research to patient care

Part IV: Enrichment & Detection Strategies

13 Immunoaffinity mass spectrometry diagnostic tests for multi-biomarker assays

14 Secretome profile of leukocyte-platelet rich fibrin (L-PRF) membranes

15 Quantification of proteins in blood by absorptive microtiter plate-based affinity purification coupled to liquid chromatography-mass spectrometry

16 Glycomics-assisted Glycoproteomics Enables Deep and Unbiased N-Glycoproteome Profiling of Complex Biological Specimens

17 The Small Protein Enrichment Assay (SPEA) for analysis of low abundance peptide hormones in plasma

Part V: Analysis of Extracellular Vesicles from Blood

18 In-depth proteomic analysis of blood circulating small extracellular vesicles

19 Protocol for Plasma Extracellular Vesicle and Particle Isolation and Mass Spectrometry-based Proteomic Identification

20 Analysis of Extracellular Vesicle and Contaminant Markers in Blood Derivatives Using Multiple Reaction Monitoring.

21 Generation of red blood cell nanovesicles as a delivery tool

Part VI: Targeted-based Mass Spectrometry

22 "Progress in targeted mass spectrometry (parallel accumulation-serial fragmentation) and its application in plasma/serum proteomics

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23 Offline peptide fractionation and parallel reaction monitoring MS for the quantitation of low-abundance plasma proteins

24 Profiling Serum Intact N-Glycopeptides Using Data-Independent Acquisition Mass Spectrometry

Part VII: Assay Development in Biomarker Discovery and Translational Proteomics

25 Semi-automated lectin magnetic bead array (LeMBA) for translational serum glycoprotein biomarker discovery and validation

26 Accessing antibody-reactivities in serum or plasma to (auto-)antigens using multiplexed bead-based protein immunoassays

27 Absolute quantitative targeted proteomics assays for plasma proteins

Part VIII: Plasma-based Peptide, Lipid, and Metabolite Assays

28 Rapid and quantitative enrichment of peptides from plasma for mass spectrometric analysis.

29 Comprehensive targeted lipidomic profiling for research and clinical applications.

30 Multiplexed bead-based peptide immunoassays for the detection of antibody reactivities

31 Array-based multiplex and high-throughput serology assays

Part IX: Software and Bioinformatics for the Plasma Proteome

32 Bioinformatic tools and knowledgebases to assist generating targeted assays for plasma proteomics

33 Use of Longitudinal Serum Analysis and Machine Learning to Develop a Classifier for Cancer Early Detection