Proteomics sample preparation

Bergkvist, J., Ekstrom, S., Wallman, L., Lofgren, M., Marko-Varga, G., Nilsson, J., and Laurell, T. (2002). Improved chip design for integrated solid-phase microextraction in on-line proteomic sample preparation. Proteomics 2, 422—429. 

Wang H, Qian WJ, Mottaz HM, Clauss TR, Anderson DJ, Moore RJ, Camp DG, 2nd, Khan AH, Sforza DM, PaUavicini M, Smith DJ, Smith RD (2005) Development and evaluation of a micro- and nanoscale proteomic sample preparation method. J Proteome Res 4 2397-2403. 

H. Moon, A.R. Wheeler, R.L. Garrell, J.A. Loo, and C-J Kim, An integrated digital microfluidic chip for multiplexed proteomic sample preparation and analysis by MADDA-MS. Lab Chip 6, 1213-1219 (2006). 

Given the complexity of most biological samples, sample preparation has been, and will be, one of the critical challenges in bioanalysis [1]. A general flow of proteomic sample preparation steps with subsequent detection is shown in Fig. 1. 

Biosample Preparation by Lab-on-a-Chip Devices, Fig. 1 General proteomic sample preparation flow... 

Microfluidic engineering has the potential to improve the proteomic sample preparation processes significantly, by the automation and integration of many, laborious fractionation steps on a chip. While microfluidic devices for 2D protein separation [6] have already been demonstrated, the following technical issues still need to be addressed before the wider application of microfluidic 2D protein separation devices. 

Zolotaijova, N. Boyes, B. MartoseUa, J. Yang, L.-S. Nicol, G. Zhang, K. Szafranski, C. Bailey, J. Immunoaffinity depletion of high-abundant proteins for proteomic sample preparation. In Separation Methods in Proteomics CRC Press Boca Raton, 2006 63-79. 

Zolotarjova N, Boyes B, Martosella J. Immunoaffinity depletion of high-abundant proteins for proteomic sample preparation. In Smqkal GB, Lazarev A, editors. Separation methods in proteomics. Boca Raton, FL CRC Press 2006. p. 63—79. Moser AC, AC, Hage DS, DS. Chromatographic immunoassays. In Hage DS, editor. Handbook of affinity chromatography. 2nd ed. Boca Raton, FL CRC Press 2005. p. 789-836. 

The results for bacterial whole-cell analysis described here establish the utility of MALDI-FTMS for mass spectral analysis of whole-cell bacteria and (potentially) more complex single-celled organisms. The use of MALDI-measured accurate mass values combined with mass defect plots is rapid, accurate, and simpler in sample preparation then conventional liquid chromatographic methods for bacterial lipid analysis. Intact cell MALDI-FTMS bacterial lipid characterization complements the use of proteomics profiling by mass spectrometry because it relies on accurate mass measurements of chemical species that are not subject to posttranslational modification or proteolytic degradation. 

Wang, H., Hanash, S. (2005). Intact-protein based sample preparation strategies for proteome analysis in combination with mass spectrometry. Mass Spectrom. Rev. 24, 413 126. 

The European Molecular Biology Laboratory s (EMBL s) offers a well-equipped pro-teomics laboratory in its facilities at the Proteomics Visitor Facility (Heidelberg, Germany). The services in MB concern protein isolation, imaging, and robotics sample preparation, supported by some other analytical facilities. 

Stewart NA, Veenstra TD. Sample preparation for mass spectrometry analysis of formalin-fixed paraffin-embedded tissue proteomic analysis of formalin-fixed tissue. Methods Mol. Biol. 2008 425 131-138. 

Several proteomic studies using archival FFPE tissues have been reported in recent years. Some involve the analysis of very small tissue samples prepared... 

In one study by Hood et al., 282 of 1153 identified proteins were identified by at least 2 unique tryptic peptides from FFPE prostate cancer (PCa) tissue.9 According to the gene ontology classification of the proteins identified, -65% of proteins were predicted to be intracellular proteins, while -50% of the total human proteome is predicted to be located in the intracellular compartment. Additionally, 20% of the proteins identified in the PCa tissue were classified as membrane proteins, which is significantly less than the predicted 40% for the human proteome. This relative disparity is not unexpected, considering the Liquid Tissue sample preparation kit lacks specific protocols for membrane protein extraction. The Liquid Tissue method has also been used for proteomics studies of a variety of FFPE tissue samples, including pancreatic tumors,28 squamous cell carcinoma,4 and oral human papillomavirus lesions.27... 

J. Gobom, M. Schuerenberg, M. Mueller, D. Theiss, H. Lehrach, and E. Nordhoff. a-Cyano-4-hydroxycinnamic Acid Affinity Sample Preparation. A Protocol for MALDI-MS Peptide Analysis in Proteomics. Anal. Chem., 73(2001) 434-438. 

The dynamic range of protein expression represents a main obstacle since abundant proteins are seldom of interest and others such as transcription factors are only present in a few copies. There is no detector that is able to visualize all proteins at the same time so that prefractionation and the investigation of subproteomes is required. In fact, pre-MS sample preparation techniques exploiting electrophoretic, chromatographic, or chemical properties of the analyte are often the bottleneck of proteomics. 

Description of LC-MS, including free articles. This site has subdivisions such as proteomics, metabonomics, 2D-electrophoresis, and sample preparation. 

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