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Pre-Clinical Models pp 3–39Cite as

A Guide to Mass Spectrometry-Based Quantitative Proteomics

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Part of the book series: Methods in Molecular Biology ((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.

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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

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Acknowledgments

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

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The authors declare no conflict of interest.

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Authors and Affiliations

  1. Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil

    Bradley J. Smith, Daniel Martins-de-Souza & Mariana Fioramonte

  2. Center for Neurobiology, University of Campinas (UNICAMP), Campinas, Brazil

    Daniel Martins-de-Souza

  3. Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Sao Paulo, Brazil

    Daniel Martins-de-Souza

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  1. Bradley J. Smith
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  2. Daniel Martins-de-Souza
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  1. Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil

    Paul C. Guest

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Smith, B.J., Martins-de-Souza, D., Fioramonte, M. (2019). A Guide to Mass Spectrometry-Based Quantitative Proteomics. In: Guest, P. (eds) Pre-Clinical Models. Methods in Molecular Biology, vol 1916. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8994-2_1

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