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A Guide to Mass Spectrometry-Based Quantitative Proteomics

  • Bradley J. Smith
  • Daniel Martins-de-Souza
  • Mariana Fioramonte
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1916)

Abstract

Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.

Key words

Quantitative proteomics Label-free Mass spectrometry Stable isotope labeling 

Abbreviations

AIF

All-ion fragmentation

AQUA

Absolute quantification

CAD

Collision-activated dissociation

CE

Collision energy

DDA

Data-dependent acquisition

DIA

Data-independent acquisition

dNSAF

Distributed normalized spectral abundance factor

emPAI

Exponentially modified protein abundance index

FT-ARM

Fourier transform-all reaction monitoring

HDMSE

High-definition MSE

iBAQ

Intensity-based absolute quantification

ICPL

Isotope-coded protein label

IMS

Ion mobility separation

LRP

Labeled reference peptide

MRM

Multiple reaction monitoring

MSE

DIA method from Waters Co.

MSX

Multiplexed MS/MS

mTRAQ

Mass-differential tags for relative and absolute quantitation

NSAF

Normalized spectral abundance factor

PSAQ

Protein standard absolute quantification

pSILAC

Pulsed stable isotope labeling of amino acids in cell culture

QconCAT

Quantitative concatemers

QQQ

Triple quadrupole

SID

Standard isotope dilution

SILAM

Stable isotope labeling of amino acids in mammals

SILIP

Stable isotope labeling in planta

SIN

Normalized spectral index

SPS-MS3

Synchronous precursor selection MS/MS/MS

TMT

Tandem mass tags

UDMSE

Ultra-definition MSE

XDIA

Extended data-independent acquisition

XIC

Extracted ion chromatogram

Notes

Acknowledgments

BJS, MF, and DMS would like to thank FAPESP for funding (under grant numbers2016/07948-8, 2016/18715-4, and 2013/08711-3).

Conflict of Interest

The authors declare no conflict of interest.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Bradley J. Smith
    • 1
  • Daniel Martins-de-Souza
    • 1
    • 2
    • 3
  • Mariana Fioramonte
    • 1
  1. 1.Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of BiologyUniversity of Campinas (UNICAMP)CampinasBrazil
  2. 2.Center for Neurobiology, University of Campinas (UNICAMP)CampinasBrazil
  3. 3.Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Cientifico e TecnologicoSao PauloBrazil

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