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Sample Preparation Focusing on Plant Omics

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Emerging Sample Treatments in Proteomics

Part of the book series: Advances in Experimental Medicine and Biology ((PMISB,volume 1073))

Abstract

Because of strong impact of omics in many fields, and the complexity of the samples when focusing on areas such as genomics, (metallo)proteomics, metabolomics, among others, it is easy to rationalize the great importance that sample preparation has for achieving reliable results, mainly considering plant science. Then, this chapter points out applications of the sample preparation focusing on such areas, and a diversity of strategies, techniques, and procedures is highlighted and commented.

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Abbreviations

AAM:

Ammonium acetate/methanol

ADP:

Adenosine diphosphate

ATP:

Adenosine triphosphate

BIF:

Banded iron formation

CE-ICP-MS:

Capillary electrophoresis-inductively coupled plasma-mass spectrometry

DNA:

Deoxyribonucleic acid

ESI-MS:

Electrospray ionization mass spectrometry

ESI-FAIMS-IT-MS:

Electrospray ionization-high-field asymmetric waveform ion mobility spectrometry-ion trap mass spectrometry

FRET:

Fluorescence resonance energy transfer

FT-ICR MS:

Fourier transform ion cyclotron resonance mass spectrometry

HPLC-DAD:

High-performance liquid chromatography with diode array detector

HPLC-DAD-ESI-MS/MS:

High-performance liquid chromatography with diode array detector coupled to electrospray ionization tandem mass spectrometry

HPLC-UV:

High-performance liquid chromatography with ultraviolet detector

HRE:

Heat reflux extraction

ICAT:

Isotope-coded affinity

ICP-MS:

Inductively coupled plasma mass spectrometry

IEF:

Isoelectric focusing

iTRAQ:

Isobaric tags for relative and absolute quantification

JA:

Jasmonic acid

LC:

Liquid chromatography

LC-ESI-MS/MS:

Liquid chromatography coupled to electrospray ionization tandem mass spectrometry

LC-ICP-MS:

Liquid chromatography-inductively coupled plasma mass spectrometry

LC-MS/MS:

Liquid chromatography tandem-mass spectrometry

LC-MS:

Liquid chromatography mass spectrometry

MAE:

Microwave-assisted extraction

MALDI-MS:

Matrix-assisted laser desorption/ionization coupled mass spectrometry

ME:

Maceration

MS:

Mass spectrometry

MTBE:

Methyl tert-butyl ether

MUDPIT:

Multidimensional protein identification technology

NADP:

Nicotinamide adenine dinucleotide phosphate

nanoESI-Q-TOF:

Nano-electrospray ionization quadrupole time-of-flight

nanoSIMS:

Nanoscale secondary ion mass spectrometry

NMR:

Nuclear magnetic resonance

PARC:

PEI-assisted RuBisCO cleanup

PEI:

Polyethylenimine

PEG:

Polyethylene glycol

pI:

Point isoelectric

PM:

Sodium phosphate/methanol

PR:

Pathogenesis related

PTMs:

Posttranslational modifications

RP-HPLC:

Reversed-phase chromatography

RP-HPLC-UV-ESI-MS:

Reversed-phase high-performance liquid chromatography-ultraviolet-electrospray ionization mass spectrometry

RuBisCO:

Ribulose-1,5-bisphosphate carboxylase/oxygenase

SEC-UV:

Size exclusion chromatography-ultraviolet

SDS-PAGE:

Sodium dodecyl sulfate polyacrylamide gel electrophoresis

(TAP)-MS:

Tandem affinity purification mass spectrometry

TCA:

Trichloroacetic acid

UAE:

Ultrasound-assisted extraction

UHPLC-DAD-ESI-MS/MS:

Ultrahigh-performance liquid chromatography with diode array detector coupled to electrospray ionization tandem mass spectrometry

UHPLC-HR-MS:

Ultrahigh-performance liquid chromatography coupled with high-resolution mass spectrometry

WM:

Water/methanol

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Acknowledgments

The authors gratefully acknowledge the financial support of Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and Financiadora de Estudos e Projetos (FINEP).

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  1. Universidade Estadual de Campinas – Unicamp, Campinas, Brazil

    Rodrigo Moretto Galazzi, Jemmyson Romário de Jesus & Marco Aurélio Zezzi Arruda

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  1. Rodrigo Moretto Galazzi
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  2. Jemmyson Romário de Jesus
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  3. Marco Aurélio Zezzi Arruda
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Correspondence to Marco Aurélio Zezzi Arruda .

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  1. BIOSCOPE Group, LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Proteomass Scientific Society, Rua dos Inventores, Madan Park, Caparica, Portugal

    José-Luis Capelo-Martínez

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Galazzi, R.M., de Jesus, J.R., Arruda, M.A.Z. (2019). Sample Preparation Focusing on Plant Omics. In: Capelo-Martínez, JL. (eds) Emerging Sample Treatments in Proteomics. Advances in Experimental Medicine and Biology(), vol 1073. Springer, Cham. https://doi.org/10.1007/978-3-030-12298-0_7

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