Abstract
Proteomics holds great promise for uncovering disease-related markers and mechanisms in human disorders. Recent advances have led to efficient, sensitive, and reproducible methods to quantitate the proteome in biological samples. Here we describe the techniques for processing, running, and analyzing samples from HIV-infected plasma or serum through quantitative mass spectroscopy.
Nicole A. Haverland and Lance M. Villeneuve have equally contributed to this chapter.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Pernemalm M, Lehtio J (2014) Mass spectrometry-based plasma proteomics: state of the art and future outlook. Expert Rev Proteomics 11(4):431–448
Anderson L (2014) Six decades searching for meaning in the proteome. J Proteomics 107C:24–30
Burkhard PR, Rodrigo N, May D, Sztajzel R, Sanchez JC, Hochstrasser DF, Schiffer E, Reverdin A, Lacroix JS (2001) Assessing cerebrospinal fluid rhinorrhea: a two-dimensional electrophoresis approach. Electrophoresis 22(9):1826–1833
Vejda S, Posovszky C, Zelzer S, Peter B, Bayer E, Gelbmann D, Schulte-Hermann R, Gerner C (2002) Plasma from cancer patients featuring a characteristic protein composition mediates protection against apoptosis. Mol Cell Proteomics 1(5):387–393
DeSouza LV, Siu KW (2013) Mass spectrometry-based quantification. Clin Biochem 46(6):421–431
Gillet LC, Navarro P, Tate S, Rost H, Selevsek N, Reiter L, Bonner R, Aebersold R (2012) Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 11(6):O111.016717
Wisniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6(5):359–362
Scopes RK (1974) Measurement of protein by spectrophotometry at 205 nm. Anal Biochem 59(1):277–282
Baldi P, Long AD (2001) A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17(6):509–519
Kayala MA, Baldi P (2012) Cyber-T web server: differential analysis of high-throughput data. Nucleic Acids Res 40(Web Server issue):W553–W559
Cheadle C, Vawter MP, Freed WJ, Becker KG (2003) Analysis of microarray data using Z score transformation. J Mol Diagn 5(2):73–81
Haverland NA, Fox HS, Ciborowski P (2014) Quantitative proteomics by SWATH-MS reveals altered expression of nucleic acid binding and regulatory proteins in HIV-1-infected macrophages. J Proteome Res 13(4):2109–2119
Taylor LE, Swan T, Mayer KH (2012) HIV coinfection with hepatitis C virus: evolving epidemiology and treatment paradigms. Clin Infect Dis 55(Suppl 1):S33–S42
Deeks SG, Lewin SR, Havlir DV (2013) The end of AIDS: HIV infection as a chronic disease. Lancet 382(9903):1525–1533
Krebs FC, Miller SR, Malamud D, Howett MK, Wigdahl B (1999) Inactivation of human immunodeficiency virus type 1 by nonoxynol-9, C31G, or an alkyl sulfate, sodium dodecyl sulfate. Antiviral Res 43(3):157–173
Villeneuve LM, Stauch KL, Fox HS (2014) Proteomic analysis of the mitochondria from embryonic and postnatal rat brains reveals response to developmental changes in energy demands. J Proteomics 109C:228–239
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Haverland, N.A., Villeneuve, L.M., Ciborowski, P., Fox, H.S. (2016). The Proteomic Characterization of Plasma or Serum from HIV-Infected Patients. In: Prasad, V., Kalpana, G. (eds) HIV Protocols. Methods in Molecular Biology, vol 1354. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3046-3_20
Download citation
DOI: https://doi.org/10.1007/978-1-4939-3046-3_20
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3045-6
Online ISBN: 978-1-4939-3046-3
eBook Packages: Springer Protocols