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Label-Free Quantification by Data Independent Acquisition Mass Spectrometry to Map Cardiovascular Proteomes

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Manual of Cardiovascular Proteomics

Abstract

The large-scale identification and quantification of proteins by liquid chromatography mass spectrometry (LC MS) can be achieved by at least three general methods, categorized into targeted, data independent (DIA), and data dependent (DDA) acquisition modes. Each acquisition strategy has its own set of benefits and drawbacks, and the methods serve complementary purposes for the study of protein quantification in biological samples. While not specific to research in cardiovascular physiology, a long-standing but recently popularized proteomic approach, termed Data Independent Acquisition Mass Spectrometry (DIA-MS), promises unique strengths to complement and extend the existing capabilities of traditional “discovery” proteomic profiling by combining development of a peptide library and DIA-MS. In this chapter we will provide background on the DIA-MS technique, highlighting its fundamental differences relative to other mass spectrometry methods, and discuss important considerations for researchers interested in implementing this technique for their proteomic experiments.

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Author information

Authors and Affiliations

  1. The Advanced Clinical Biosystems Research Institute, Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA

    Sarah J. Parker PhD, Ronald J. Holewinski PhD, Irina Tchernyshyov MSc, Vidya Venkatraman MS & Jennifer E. Van Eyk PhD, FAHA, FISHR

  2. Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA

    Laurie Parker PhD

  3. Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Jennifer E. Van Eyk PhD, FAHA, FISHR

Authors
  1. Sarah J. Parker PhD
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  2. Ronald J. Holewinski PhD
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  3. Irina Tchernyshyov MSc
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  4. Vidya Venkatraman MS
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  5. Laurie Parker PhD
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  6. Jennifer E. Van Eyk PhD, FAHA, FISHR
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Corresponding author

Correspondence to Sarah J. Parker PhD .

Editor information

Editors and Affiliations

  1. Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Giulio Agnetti

  2. Dept. of Physiology & Biophysics, University Mississippi Medical Center, Jackson, Mississippi, USA

    Merry L. Lindsey

  3. Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    D. Brian Foster

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© 2016 Springer International Publishing Switzerland

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Parker, S.J., Holewinski, R.J., Tchernyshyov, I., Venkatraman, V., Parker, L., Van Eyk, J.E. (2016). Label-Free Quantification by Data Independent Acquisition Mass Spectrometry to Map Cardiovascular Proteomes. In: Agnetti, G., Lindsey, M., Foster, D. (eds) Manual of Cardiovascular Proteomics. Springer, Cham. https://doi.org/10.1007/978-3-319-31828-8_10

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  • DOI: https://doi.org/10.1007/978-3-319-31828-8_10

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-31826-4

  • Online ISBN: 978-3-319-31828-8

  • eBook Packages: MedicineMedicine (R0)

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