Quantitative Proteomics

Claire E Eyers, Simon Gaskell

• Publisher: Royal Society of Chemistry
• Year: 2014
• eBook ISBN: 9781782621096
• Edition: 1
• Topic: Physical Sciences
• Subtopic: Biology

As a component of post-genome science, the field of proteomics has assumed great prominence in recent years. Whereas quantitative analyses focussed initially on relative quantification, a greater emphasis is now placed on absolute quantification and consideration of proteome dynamics. Coverage of the topic of quantitative proteomics requires consideration both of the analytical fundamentals of quantitative mass spectrometry and the specific demands of the problem being addressed.

Quantitative Proteomics aims to outline the state of the art in mass spectrometry-based quantitative proteomics, describing recent advances and current limitations in the instrumentation used, together with the various methods employed for generating high quality data. Details on both strategies describing how stable isotope labelling can be applied and methods for performing quantitative analysis of proteins in a label-free manner are given. The utility of these strategies to understanding cellular protein dynamics are then exemplified with chapters looking at spatial proteomics, dynamics of protein function as determined by quantifying changes in protein post-translational modification and protein turnover. Finally, a key application of these techniques to biomarker discovery and validation is presented, together with the rapidly developing area of quantitative analysis of protein-based foodstuffs.

This exemplary book is essential reading for analytical and biological mass spectrometrists working in proteomics research, as well as those undertaking either fundamental or clinical-based investigations with an interest in understanding protein dynamics and/or biomarker assessment.

Subject Index

3T3-L1 adipocytes 221

β-elimination reactions 331

Δr (desolvation distance) 9

a priori knowledge, SRM assays 85–7

AAA (amino acid analysis) 112

AAL (Aleuria aurantia lectin) 164, 165, 166–7

absolute protein abundance index (APEX) 95

absolute protein quantification

applications 81–2

challenges

complete protein extraction 96–7

optimal peptide selection 98–100

specific/complete protein digestion 97–8

translation of label-free MS intensities into absolute protein quantities 100–1

ICP-MS method 118–25

LC–MS/MS workflows 4, 5–6

need for 80–3

phosphorus-quantified phosphopeptide standards 113–16

peptide/phosphopeptide ratio standards 118

phosphorus-free 116–17

selected reaction monitoring 80–103

selenium-quantified but selenium-free protein standards 123–5

targeted mass spectrometry 83–8

technologies 82–3

tyrosine phosphorylation 223, 224

absolute quantification (AQUA) peptides 90

abundances of proteins, LC–MS/MS 16

accuracy

isobaric tag methods 59–62, 71, 243

LOPIT 202

MS^E data-independent acquisition 182

spatial dynamic proteomics 203, 205

synthetic peptide standards 91

accurate mass and retention time alignment (AMRT) 139, 140, 141

acetylation, primary amines 54

acetyllysine-containing peptides 157

actin cytoskeletons 65

adherens junctions 188

adipocytes 221

ADP-ribosylated PTMs enrichment 248

agarose beads 215

alcohol dehydrogenase (ADH) 149

Aleuria aurantia lectin (AAL) 164, 165, 166–7

allergens detection in food 337–44

Amadori products 331

amine-specific tandem mass tags 58

amines, primary, acetylation 54

amino acid analysis (AAA) 112

AMRT (accurate mass and retention time alignment) 139, 140, 141

analyte concentrations/ionisation efficiency 9

analytical fractionation method 198

anchor proteins 100, 101

animal models

mouse

anemia 322–3

leptin 319

liver 157, 261

whole brain lysis 182

SILAC labelling 197

annotation

food proteome 330–1

gene ontology annotation 196, 205–6, 227, 290–1

antibodies

absolut...

Table of contents

• Cover
• Title
• Copyright
• Contents
• Preface
• Technology
• Label-based Protein Quantification
• Label-free Protein Quantification
• Dynamic Protein Quantification
• Applications of Quantitative Proteomics
• Subject Index