Liquid Chromatography Proteomics

Szponarski, W., Sommerer, N., Boyer, J.C., Rossignol, M. and Gibrat, R. (2004) Large-scale characterization of integral proteins from Arabidopsis vacuolar membrane by two-dimensional liquid chromatography. Proteomics 4, 397 06. 

The Tools of Proteomics A variety of methods and techniques including two-dimensional gel electrophoresis (2DE), capillary liquid chromatography, stable isotope labeling, and mass spectrometry has been developed for qualitative and quantitative protein... 

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. 

Dunlop, K. Y. Li, L. Automated Mass Analysis of low-molecular-mass bacterial proteome by liquid chromatography-electrospray ionization mass spectrometry. J. Chromatogr. A 2001, 925,123-132. 

Shen, Y., Tolic, N., Zhao, R., Pasa-Tolic, L., Li, L., Berger, S.J., Harkewicz, R., Anderson, G.A., Belov, M.E., Smith, R.D. (2001). High-throughput proteomics using high efficiency multiple-capillary liquid chromatography with on-line high performance ESI FTICR mass spectrometry. Anal. Chem. 73, 3011-3021. 

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. 

FIGURE 9.1 Liquid chromatography workflow strategy options in proteomics. (a) bottom-up approach (b) top-down approach (c) selective sample cleanup directly combined with chromatographic separation (d) peptide capture with affinity restricted access material. 

Blonder, J., Rodriguez-Galan, M.C., Chan, K.C., Lucas, D.A., Yu, L.R., Conrads, T.P, Issaq, H. J., Young, H.A., Veenstra, T.D. (2004). Analysis of murine natural killer cell microsomal proteins using two-dimensional liquid chromatography coupled to tandem electrospray ionization mass spectrometry. J. Proteome Res. 3, 862-870. 

Chen, J., Lee, C.S., Shen, Y., Smith, R.D., Baehrecke, E.H. (2002). Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation. Electrophoresis 23, 3143-3148. 

DeSouza, L., Diehl, G., Rodrigues, M.J., Guo, J., Romaschin, A.D., Colgan, T.J., Siu, K.W. (2005). Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res. 4, 377-386. 

Gaucher, S.P., Taylor, S.W., Fahy, E., Zhang, B., Wamock, D.E., Ghosh, S.S., Gibson, B.W. (2004). Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometry. J. Proteome Res. 3, 495-505. 

Gu, S Du, Y Chen, J., Liu, Z Bradbury, E.M., Hu, C.A., Chen, X. (2004). Large-scale quantitative proteomic study of PUMA-induced apoptosis using two-dimensional liquid chromatography—mass spectrometry coupled with amino acid-coded mass tagging. J. Proteome Res. 3, 1191 1200. 

Mawuenyega, K.G., Kaji, H., Yamuchi, Y., Shinkawa, T., Saito, H., Taoka, M., Takahashi, N., Isobe, T. (2003). Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography—tandem mass spectrometry. J. Proteome Res. 2, 23-35. 

Nagele, E., Vollmer, M., Horth, P. (2003). Two-dimensional nano-liquid chromatography— mass spectrometry system for applications in proteomics. J. Chromatogr. A1009,197-205. 

Tyan, Y.C., Wu, H.Y., Lai, W.W., Su, W.C., Liao, PC. (2005b). Proteomic profiling of human pleural effusion using two-dimensional nano liquid chromatography tandem mass spectrometry. J. Proteome Res. 4, 1274-1286. 

Wehr, T. (2002). Multidimensional Liquid Chromatography in Proteomic Studies. LCGCNorth America 20, 954-962. 

Whitelegge, J.P, Zhang, H., Aguilera, R., Taylor, R.M., Cramer, W.A. (2002). Full subunit coverage liquid chromatography electrospray ionization mass spectrometry (LCMS+) of an oligomeric membrane protein cytochrome b(6)f complex from spinach and the cyanobacterium Mastigocladus laminosus. Mol. Cell. Proteomics. 1, 816-827. 

At least two driving forces have contributed to the recent increased use and development of multidimensional liquid chromatography (MDLC). These include the high resolution and peak capacity needed for proteomics studies and the independent size and chemical structure selectivity for resolving industrial polymers. In this regard, separation science focuses on a system approach to separation as individual columns can contribute only part of the separation task and must be incorporated into a larger separation system for a more in-depth analytical scheme. 

Methods based on liquid chromatography-mass spectrometry (LC-MS) and universally accepted search algorithms permit reliable identifications of low levels of proteins at high sensitivity [6]. Even semispecialized protein chemistry labs can readily identify proteins at the level of a few picomoles (10 pmol of a 50-kDa protein is 500 ng). Specialized groups with access to the latest advances in HPLC and mass spectrometry routinely work with subpicomolar quantities. Chemical proteomics as discussed here requires the more advanced equipment. 

Wang W, Guo T, Rudnick PA, et al. Membrane proteome analysis of micro-dissected ovarian tumor tissues using capillary isoelectric focusing/reversed-phase liquid chromatography-tandem MS. Anal. Chem. 2007 79 1002-1009. 

Introduces microparallel liquid chromatography (LC), ADME/PK high-throughput assay, MS-based proteomics, and the advances of capillary and nano-HPLC technology... 

I. D. Wilson, J. K. Nicholson, J. Castro-Perez, J. H. Granger, K. A. Johnson, B. W. Smith, and R. S. Plumb. High Resolution Ultra Performance Liquid Chromatography Coupled to oa-TOF Mass Spectrometry as a Tool for Differential Metabolic Pathway Profiling in Functional Genomic Studies. J. Proteome Res., 4(2005) 591-598. 

M. Ramstrom, I. Ivonin, A. Johansson, H. Askmark, K. E. Markides, R. Zubarev, P. Hakansson, S.-M. Aquilonius, and J. Bergquist. Cerebrospinal Fluid Protein Patterns in Neurodegenerative Disease Revealed by Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Proteomics, 4(2004) 4010-4018. 

Lazar, I. M., Trisiripisal, P., and Sarvaiya, H. A. (2006). Microfluidic liquid chromatography system for proteomic applications and biomarker screening. Anal. Chem. 78, 5513—5524. 

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