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Proteomics in heart failure: top-down or bottom-up?

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Abstract

The pathophysiology of heart failure (HF) is diverse, owing to multiple etiologies and aberrations in a number of cellular processes. Therefore, it is essential to understand how defects in the molecular pathways that mediate cellular responses to internal and external stressors function as a system to drive the HF phenotype. Mass spectrometry (MS)-based proteomics strategies have great potential for advancing our understanding of disease mechanisms at the systems level because proteins are the effector molecules for all cell functions and, thus, are directly responsible for determining cell phenotype. Two MS-based proteomics strategies exist: peptide-based bottom-up and protein-based top-down proteomics—each with its own unique strengths and weaknesses for interrogating the proteome. In this review, we will discuss the advantages and disadvantages of bottom-up and top-down MS for protein identification, quantification, and analysis of post-translational modifications, as well as highlight how both of these strategies have contributed to our understanding of the molecular and cellular mechanisms underlying HF. Additionally, the challenges associated with both proteomics approaches will be discussed and insights will be offered regarding the future of MS-based proteomics in HF research.

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Abbreviations

HF:

Heart failure

MS:

Mass spectrometry

PTMs:

Post-translational modifications

2DGE:

Two-dimensional gel electrophoresis

m/z :

Mass-to-charge ratio

MS/MS:

Tandem mass spectrometry

MALDI:

Matrix-assisted laser desorption/ionization

ESI:

Electrospray ionization

LC:

Liquid chromatography

CID:

Collision-induced dissociation

AP:

Affinity purification

ECD:

Electron capture dissociation

SNO:

S-nitrosylation

cTnI:

Cardiac troponin I

SHR:

Spontaneously hypertensive rat

WKY:

Wistar-Kyoto

iTRAQ:

Isotope tags for relative and absolute quantification

MI:

Myocardial infarction

SILAC:

Stable isotope labeling by amino acids in cell culture

TAC:

Transverse aortic constriction

MW:

Molecular weight

MDLC:

Multi-dimensional liquid chromatography

cMyBP-C:

Cardiac myosin binding protein-C

TOF:

Time-of-flight

Q-TOF:

Quadrupole-time-of-flight

HCD:

High-energy collision dissociation

IRMPD:

Infrared multiphoton dissociation

UVPD:

Ultraviolet photodissociation

PSD:

Post-source decay

ETD:

Electron transfer dissociation

GELFrEE:

Gel-eluted liquid fraction entrapment electrophoresis

IMAC:

Immobilized-metal affinity chromatography

TMT:

Tandem mass tag

FTMS:

Fourier-transform mass spectrometry

iCAT:

Isotope-coded affinity tag

HDAC:

Histone deacetylase

Tm:

Tropomyosin

XIC:

Extracted ion chromatogram

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Acknowledgments

We would like to acknowledge the financial support by the National Institute of Health R01HL096971 and R01HL109810 (to YG). ZG would like to thank the National Institute of Health training grant T32GM008688.

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Authors and Affiliations

  1. Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA

    Zachery R. Gregorich & Ying Ge

  2. Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA

    Zachery R. Gregorich, Ying-Hua Chang & Ying Ge

  3. Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA

    Ying-Hua Chang & Ying Ge

  4. Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA

    Ying Ge

  5. 1300 University Ave., SMI 130, Madison, WI, USA

    Ying Ge

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  1. Zachery R. Gregorich
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  2. Ying-Hua Chang
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Correspondence to Ying Ge.

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Gregorich, Z.R., Chang, YH. & Ge, Y. Proteomics in heart failure: top-down or bottom-up?. Pflugers Arch - Eur J Physiol 466, 1199–1209 (2014). https://doi.org/10.1007/s00424-014-1471-9

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