Proteomics high-performance liquid chromatography

Kaliszan, R., Baczek, T., Cimochowska, A., Juszczyk, P., Wisniewska, K., Grzonka, Z. Prediction of high-performance liquid chromatography retention of peptides with the use of quantitative structure-retention relatiorrships. Proteomics 2005, 5, 409 15. 

Opiteck, G. J. Ramirez, S. M. Jorgenson, J. W. Moseley, M. A., 3rd. Comprehensive two-dimensional high-performance liquid chromatography for the isolation of overexpressed proteins and proteome mapping. Anal. Biochem. 1998,258,349-361. 

Premstaller, A., Oberacher, H., Walcher, W., Timperio, A.M., Zolla, L., Chervet, J.P., Cavusoglu, N., van Dorsselaer, A., Huber, C.G. (2001). High-performance liquid chromatography-electrospray ionization mass spectrometry using monolithic capillary columns for proteomic studies. Anal. Chem. 73, 2390-2396. 

The peptide mixture that results from tryptic digestion of a protein mixmre is usually fractionated prior to being submitted to mass spectrometric analysis. The goal of the separation is to reduce the complexity of the peptide mixmre to simplify analysis of peptide mass peaks. The most commonly used method in exosome proteome studies is reverse phase high performance liquid chromatography (Feviier et al. 2004 Pisitkun et al. 2004 Potolicchio et al. 2005 Segura et al. 2005 Faure et al. 2006). For this method, a mixture of peptides in aqueous solution is loaded onto a colurrm packed with... 

The methods for each study are divided into the initial protein separation step, a second separation step if applicable, the type of mass analysis, and the software used for peptide identification. ID = one dimensional polyacrylamide gel electrophoresis, 2D = two dimensional polyacrylamide gel electrophoresis, MS = mass spectrometry (peptide mass fingerprinting), MS/MS = tandem mass spectrometry, MALDI-TOF = matrix assisted laser desorption/ionization-time of flight, MS FIT = software from Protein Prospector, http //prospector.ucsf edu/, ESI = electrospray ionization, Q-TOF = quadrupole-time of flight, PPSS2 =Protana s Proteomic Software Suite (ProtanaEngineering, Odense, Denmark), Mascot = Matiix Science, http //www.matrixscience.com/, TOF-TOF = MALDI plus TOF tandem mass spectrometry, RP-HPLC = reverse phase high performance liquid chromatography, Q-IT = quadrupole ion trap, LIT = linear ion trap. Bioworks = Thermo Electron Corporation. 

Fung, K.Y.C., Askovic, S., Basile, F. and Duncan, M.W. (2004) A simple and inexpensive approach to interfacing high-performance liquid chromatography and matrix-assisted laser desorption/ionization-time of flight-mass spectrometry. Proteomics 4, 3121-3127. 

Rudd PM, Colominas C, Royle L, Murphy N, Hart E, Merry AH, Hebestreit HF, Dwek RA. A high-performance liquid chromatography based strategy for rapid, sensitive sequencing of N-linked oligosaccharide modifications to proteins in sodium do-decyl sulphate polyacrylamide electrophoresis gel bands. Proteomics 2001 1 285-294. 

Yang, J. et al., High performance liquid chromatography-mass spectrometry for metabonomics Potential biomarkers for acute deterioration of liver function in chronic hepatitis B, J. Proteome Res., 5(3), 554, 2006. 

Current proteomic methods of protein separation by 2D gel and/or high-performance liquid chromatography (HPLC), as well as the identification of proteins by mass spectrometry (MS) in conjunction with protein databanks and several software programs are satisfactory. These methods must be improved in the future to be more efficient. Some improvements that are expected in the near future must include the following strategies as discussed by others as well ... 

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