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Depletion of Myofibril-Associated Proteins Using Selective Protein Extraction as a Tool in Cardiac Proteomics

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Tissue Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1788))

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Abstract

Muscle tissue poses a particular challenge to proteomic analysis due to a very wide range of protein abundances arising from the dominant expression of myofilament-related proteins. We address this issue by describing proteomic analysis with liquid chromatography–mass spectrometry (LC-MS) and sequential window acquisition of all theoretical mass spectra (SWATH), of guinea pig cardiac tissue prepared in two homogenization buffers: (1) An SDS-based buffer designed to extract “all” tissue proteins and (2) a long-established EDTA-containing buffer thought to preferentially extract non-myofibril-related proteins. We use gene ontology (GO) annotation-based assessment of subcellular localization to indicate if these enriched proteins congregate in the cytoplasm or in organellar lumens. This technique results in the preferential quantitation of less abundant non-myofibrillar proteins and, for future studies, offers the opportunity for more complete analyses of changes in heart tissue protein expression with biological circumstance.

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Acknowledgments

This work was supported by the Medical Research Council (MR/L009560/1 and G0902091). The authors would like to thank Sir Philip Cohen for helpful discussions.

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Authors and Affiliations

  1. Newcastle University Protein and Proteome Analysis, Newcastle University, Cookson Building, Medical School, University of Newcastle, NE2 4HH, UK

    Achim Treumann

  2. Cardiovascular Research Centre, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK

    Achim Treumann, Pawel Palmowski, Wing Chiu Tong, Julie Taggart, G. Nicholas Europe-Finner & Michael J. Taggart

  3. Nick Morrice, ABSciex, Warrington, WA1 1RX, UK

    Nick Morrice

Authors
  1. Achim Treumann
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  2. Pawel Palmowski
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  3. Wing Chiu Tong
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  4. Julie Taggart
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  5. Nick Morrice
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  6. G. Nicholas Europe-Finner
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  7. Michael J. Taggart
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Corresponding author

Correspondence to Achim Treumann .

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Editors and Affiliations

  1. Professor, Department of Surgery Medicine and Pediatrics Director, Kidney-Pancreas Transplant Program, University of California San Francisco, San Francisco, California, USA

    Minnie M. Sarwal

  2. Asst. Professor, Department of Surgery, University of California San Francisco, San Francisco, California, USA

    Tara K. Sigdel

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© 2017 Springer Science+Business Media New York

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Treumann, A. et al. (2017). Depletion of Myofibril-Associated Proteins Using Selective Protein Extraction as a Tool in Cardiac Proteomics. In: Sarwal, M., Sigdel, T. (eds) Tissue Proteomics. Methods in Molecular Biology, vol 1788. Humana Press, New York, NY. https://doi.org/10.1007/7651_2017_73

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  • DOI: https://doi.org/10.1007/7651_2017_73

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7852-6

  • Online ISBN: 978-1-4939-7854-0

  • eBook Packages: Springer Protocols

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