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Mass Spectrometry for Proteomics-Based Investigation

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Advancements of Mass Spectrometry in Biomedical Research

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 806))

Abstract

Within the past years, we have witnessed a great improvement in mass spectrometry (MS) and proteomics approaches in terms of instrumentation, protein fractionation, and bioinformatics. With the current technology, protein identification alone is no longer sufficient. Both scientists and clinicians want not only to identify proteins but also to identify the protein’s posttranslational modifications (PTMs), protein isoforms, protein truncation, protein–protein interaction (PPI), and protein quantitation. Here, we describe the principle of MS and proteomics and strategies to identify proteins, protein’s PTMs, protein isoforms, protein truncation, PPIs, and protein quantitation. We also discuss the strengths and weaknesses within this field. Finally, in our concluding remarks we assess the role of mass spectrometry and proteomics in scientific and clinical settings in the near future. This chapter provides an introduction and overview for subsequent chapters that will discuss specific MS proteomic methodologies and their application to specific medical conditions. Other chapters will also touch upon areas that expand beyond proteomics, such as lipidomics and metabolomics.

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Abbreviations

BN-PAGE:

Blue native PAGE

CI:

Chemical ionization

CN-PAGE:

Colorless native PAGE

DIGE:

Differential gel electrophoresis

EI:

Electron ionization

ESI:

Electrospray ionization

ESI-MS:

Electrospray ionization mass spectrometry

FT:

Fourier transform

IT:

Ion trap

LC–MS/MS:

Liquid chromatography–mass spectrometry

m/z :

Mass/charge

MALDI:

Matrix-assisted laser desorption ionization

MALDI-MS:

MALDI mass spectrometry

MS:

Mass spectrometry

Mw:

Molecular weight

Q:

Quadrupole

SDS-PAGE:

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis

TIC:

Total ion current/chromatogram

TOF:

Time of flight

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Acknowledgements

We would like to thank Ms. Laura Mulderig, Scott Nichols, and their colleagues (Waters Corporation) for their generous support in setting up the Proteomics Center at Clarkson University. CCD thanks Drs. Thomas A. Neubert (New York University), Belinda Willard (Cleveland Clinic), and Gregory Wolber and David Mclaughin (Eastman Kodak Company) for donation of a TofSpec2E MALDI-MS (each). CCD thanks his advisors, Vlad Artenie, Wolfgang Haehnel, Paul M. Wassarman, and Thomas A. Neubert, for their advice and support. This work was supported in part by the Keep a Breast Foundation (KEABF-375-35054), the Redcay Foundation (SUNY Plattsburgh), the Alexander von Humboldt Foundation, SciFund Challenge, private donations (Ms. Mary Stewart Joyce and Mr. Kenneth Sandler), the David A. Walsh fellowship, and by the U.S. Army research office (DURIP grant #W911NF-11-1-0304).

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  1. Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5810, USA

    Alisa G. Woods, Izabela Sokolowska, Armand G. Ngounou Wetie, Kelly Wormwood, Roshanak Aslebagh, Sapan Patel & Costel C. Darie

  2. Memorial Sloan Kettering Cancer Center, Molecular Pharmacology and Chemistry Program, New York, NY, USA

    Sapan Patel

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Correspondence to Costel C. Darie .

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  1. Chemistry and Biomolecular Science Biochemistry and Proteomics Group, Clarkson University, Potsdam, New York, USA

    Alisa G. Woods

  2. Chemistry and Biomolecular Science Biochemistry and Proteomics Group, Clarkson University, Potsdam, New York, USA

    Costel C. Darie

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Woods, A.G. et al. (2014). Mass Spectrometry for Proteomics-Based Investigation. In: Woods, A., Darie, C. (eds) Advancements of Mass Spectrometry in Biomedical Research. Advances in Experimental Medicine and Biology, vol 806. Springer, Cham. https://doi.org/10.1007/978-3-319-06068-2_1

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