Proteomic analysis applications

Shores, K.S. Udugamasooriya, D.G. Kodadek, T. Knapp, D.R. Use of peptide analogue diversity library beads for increased depth of proteomic analysis application to cerebrospinal fluid. J. Proteome Res. 2008, 7, 1922—1931. 

Williams, C., and Addona, T. A. (2000). The integration of SPR biosensors with mass spectrometry possible applications for proteome analysis. Trends Biotechnol. 18, 45-48. 

Aebersold, R. (2003) Quantitative proteome analysis Methods and applications. /. Infect. Dis. 187 (Suppl. 2), S315-S320. 

Mass analyzers interrogate and resolve ions produced by an ion source based on their m/z ratios. Several types of mass analyzers are utilized for proteomic analysis including time-of-flight (TOF) quadrupoles, ion traps, and Fourier transform ion cyclotron resonance (FTICR). Mass analyzers may be assembled in hybrid configurations. MS instruments such as quadrupole TOF and quadra-pole ion trap-FTICR facilitate diversified applications and achieved great success. 

Ion traps are favored for proteomics studies because of their ability to perform multistage mass analysis (MSn), thereby increasing the structural information obtained from molecules. Ion traps, however, do not provide information for ions that have lower mass-to-charge values (the one-third rule). Additionally, the sensitivity of ion traps can also be limiting because only about 50% of the ions within a trap are ejected to the detector. Ion traps are also subject to a space charging phenomenon that may occur when the concentration of ions in the trap is high and produces ion repulsion within the trap. Nevertheless, the versatility and robustness of ion trap MS underlies its popularity for several proteomics-related applications. 

R. Aebersold. Quantitative Proteome Analysis Methods and Applications. J. Infect. Dis., 187, Suppl 2(2003) S315-20. 

Liu N, Liu F, Xu B, Gao Y, Li X, Wei K, Zhang X, Yang S (2008) Establishment of imaging mass spectrometry for biological tissue and its application on the proteome analysis of micro-wave radiated hippocampus. Chin J Anal Chem 36(4) 421—425... 

In the last years the application of two-dimensional electrophoresis (2-DE) has often been declared outdated and a new century of gel-free proteomics was announced. Nevertheless, 2-DE is still the method of choice when analyzing complex protein mixtures. With a separation of10 000 proteins, 2-DE gives access to high-resolution proteome analysis. Continuous development has consolidated 2-DE application in proteomics, where the introduction of difference gel electrophoresis (DICE) is the latest improvement. DICE is based on fluorescently tagging all proteins in each sample with one set of matched fluorescent dyes designed to minimally interfere with protein mobility during 2-DE. 

In the proteomic analysis of the brain, two-dimensional gels for protein separation, followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry for protein identification, have mainly been employed. This classical proteomics approach allows for the quantification of changes in protein levels and modifications. Simultaneously, it is a robust, well-established method that finds wide application in the study of biological systems. In this article, we provide a description of the protocols of the proteomic analysis used in our laboratory and a summary of the major findings from our group and other neuroproteomics groups. 

Moritz, R.L., Clippingdale, A.B., Kapp, E.A., Eddes, J.S., Ji, H., Gilbert, S., Connolly, L.M. and Simpson, R.J. (2005) Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins. Proteomics 5, 3402-3413. 

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