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Approaches for targeted proteomics and its potential applications in neuroscience

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Abstract

An extensive guide on practicable and significant quantitative proteomic approaches in neuroscience research is important not only because of the existing overwhelming limitations but also for gaining valuable understanding into brain function and deciphering proteomics from the workbench to the bedside. Early methodologies to understand the functioning of biological systems are now improving with high-throughput technologies, which allow analysis of various samples concurrently, or of thousand of analytes in a particular sample. Quantitative proteomic approaches include both gel-based and non-gel-based methods that can be further divided into different labelling approaches. This review will emphasize the role of existing technologies, their advantages and disadvantages, as well as their applications in neuroscience. This review will also discuss advanced approaches for targeted proteomics using isotope-coded affinity tag (ICAT) coupled with laser capture microdissection (LCM) followed by liquid chromatography tandem mass spectrometric (LC-MS/MS) analysis. This technology can further be extended to single cell proteomics in other areas of biological sciences and can be combined with other ‘omics’ approaches to reveal the mechanism of a cellular alterations. This approach may lead to further investigation in basic biology, disease analysis and surveillance, as well as drug discovery. Although numerous challenges still exist, we are confident that this approach will increase the understanding of pathological mechanisms involved in neuroendocrinology, neuropsychiatric and neurodegenerative disorders by delivering protein biomarker signatures for brain dysfunction.

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Abbreviations

2-DE:

two-dimensional gel electrophoresis

2D-DIGE:

two-dimensional difference gel electrophoresis

AA:

avidin affinity

AD:

Alzheimer’s disease

CE:

cation exchange

CID:

collision-induced dissociation

CSF:

cerebrospinal fluid

Cy3:

cyanin 3

Cy5:

cyanin 5

ICAT:

isotope-coded affinity tag

iTRAQ:

isobaric tags for relative and absolute quantification

IEF:

isoelectric focusing

LC:

liquid chromatography

LCM:

laser capture microdissection

MALDI-TOF-MS:

matrix-assisted laser desorption ionization time-of-flight mass spectrometry

MS:

mass spectrometry

MS/MS:

tandem mass spectrometry

PBS:

phosphate buffer saline

PD:

Parkinson’s disease

PTM:

post-translational modification

Q-TOF:

quadrupole time-of-flight

SILAC:

stable isotope labelling with amino acids in cell culture

SILAM:

stable isotope labelling of mammals.

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  1. Brain Research Institute, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Selangor Darul Ehsan, Malaysia

    Sumit Sethi, Dipti Chourasia & Ishwar S Parhar

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  1. Sumit Sethi
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  2. Dipti Chourasia
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Corresponding editor: Neeraj Jain

[Sethi S, Chourasia D and Parhar IS 2015 Approaches for targeted proteomics and its potential applications in neuroscience. J. Biosci.] DOI 10.1007/s12038-015-9537-1

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Sethi, S., Chourasia, D. & Parhar, I.S. Approaches for targeted proteomics and its potential applications in neuroscience. J Biosci 40, 607–627 (2015). https://doi.org/10.1007/s12038-015-9537-1

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