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Modern Proteomics – Sample Preparation, Analysis and Practical Applications

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Cover of 'Modern Proteomics – Sample Preparation, Analysis and Practical Applications'

Table of Contents

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    Book Overview
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    Chapter 1 Proteomes, Their Compositions and Their Sources
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    Chapter 2 Protein Fractionation and Enrichment Prior to Proteomics Sample Preparation
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    Chapter 3 Sample Preparation for Mass Spectrometry-Based Proteomics; from Proteomes to Peptides
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    Chapter 4 Plant Structure and Specificity – Challenges and Sample Preparation Considerations for Proteomics
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    Chapter 5 Improving Proteome Coverage by Reducing Sample Complexity via Chromatography
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    Chapter 6 Database Search Engines: Paradigms, Challenges and Solutions
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    Chapter 7 Mass Analyzers and Mass Spectrometers
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    Chapter 8 Top-Down Mass Spectrometry: Proteomics to Proteoforms
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    Chapter 9 Platforms and Pipelines for Proteomics Data Analysis and Management
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    Chapter 10 Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics
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    Chapter 11 Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results
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    Chapter 12 Protein Inference
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    Chapter 13 Modification Site Localization in Peptides
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    Chapter 14 Useful Web Resources
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    Chapter 15 Mass Spectrometry-Based Protein Quantification
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    Chapter 16 Bioinformatics Tools for Proteomics Data Interpretation
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    Chapter 17 Identification, Quantification, and Site Localization of Protein Posttranslational Modifications via Mass Spectrometry-Based Proteomics
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    Chapter 18 Protein-Protein Interaction Detection Via Mass Spectrometry-Based Proteomics
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    Chapter 19 Protein Structural Analysis via Mass Spectrometry-Based Proteomics
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    Chapter 20 Introduction to Clinical Proteomics
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    Chapter 21 Discovery of Candidate Biomarkers
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    Chapter 22 Statistical Approaches to Candidate Biomarker Panel Selection
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    Chapter 23 Qualification and Verification of Protein Biomarker Candidates
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    Chapter 24 Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach
Attention for Chapter 24: Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach
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Chapter title
Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach
Chapter number 24
Book title
Modern Proteomics – Sample Preparation, Analysis and Practical Applications
Published in
Advances in experimental medicine and biology, December 2016
DOI 10.1007/978-3-319-41448-5_24
Pubmed ID
Book ISBNs
978-3-31-941446-1, 978-3-31-941448-5
Authors

Andrew J. Percy, Juncong Yang, Andrew G. Chambers, Yassene Mohammed, Tasso Miliotis, Christoph H. Borchers

Editors

Hamid Mirzaei, Martin Carrasco

Abstract

Quantitative mass spectrometry (MS)-based approaches are emerging as a core technology for addressing health-related queries in systems biology and in the biomedical and clinical fields. In several 'omics disciplines (proteomics included), an approach centered on selected or multiple reaction monitoring (SRM or MRM)-MS with stable isotope-labeled standards (SIS), at the protein or peptide level, has emerged as the most precise technique for quantifying and screening putative analytes in biological samples. To enable the widespread use of MRM-based protein quantitation for disease biomarker assessment studies and its ultimate acceptance for clinical analysis, the technique must be standardized to facilitate precise and accurate protein quantitation. To that end, we have developed a number of kits for assessing method/platform performance, as well as for screening proposed candidate protein biomarkers in various human biofluids. Collectively, these kits utilize a bottom-up LC-MS methodology with SIS peptides as internal standards and quantify proteins using regression analysis of standard curves. This chapter details the methodology used to quantify 192 plasma proteins of high-to-moderate abundance (covers a 6 order of magnitude range from 31 mg/mL for albumin to 18 ng/mL for peroxidredoxin-2), and a 21-protein subset thereof. We also describe the application of this method to patient samples for biomarker discovery and verification studies. Additionally, we introduce our recently developed Qualis-SIS software, which is used to expedite the analysis and assessment of protein quantitation data in control and patient samples.

Twitter Demographics

The data shown below were collected from the profile of 1 tweeter who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 12 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 12 100%

Demographic breakdown

Readers by professional status Count As %
Professor > Associate Professor 4 33%
Researcher 3 25%
Student > Ph. D. Student 2 17%
Other 2 17%
Lecturer > Senior Lecturer 1 8%
Other 0 0%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 5 42%
Medicine and Dentistry 2 17%
Computer Science 1 8%
Agricultural and Biological Sciences 1 8%
Psychology 1 8%
Other 2 17%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 20 December 2016.
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#7,633,353
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Outputs from Advances in experimental medicine and biology
#1,993
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Outputs of similar age from Advances in experimental medicine and biology
#329
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