Abstract
Sample preparation oftentimes can be the Achilles Heel of any analytical process, and in the field of proteomics, preparing samples for mass spectrometric analysis is no exception. Current goals, concerning proteomic sample preparation on a large scale, include efforts toward improving reproducibility, reducing the time of processing and ultimately the automation of the entire workflow. This chapter reviews an array of recent approaches applied to bottom-up proteomics sample preparation to reduce the processing time down from hours to minutes. The current state-of-the-art approaches in the field use different energy inputs such as microwave, ultrasound or pressure to perform the four basic steps in sample preparation: protein extraction, denaturation, reduction/alkylation, and digestion. No single energy input for enhancement of proteome sample preparation has become the universal gold standard. Instead, a combination of different energy inputs tends to produce the best results. This chapter further describes the future trends in the field such as the hyphenation of sample preparation with downstream detection and analysis systems. Finally, a detailed protocol describing the combined use of both pressure cycling technology and ultrasonic energy inputs to hasten proteomic sample preparation is presented.
Keywords
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- ESI:
-
Electrospray ionization
- FDR:
-
False discovery rate
- HIFU:
-
High intensity focused ultrasound
- HPP:
-
High pressure processing
- IAM:
-
Iodoacetamide
- IT:
-
Ion trap
- MAPED:
-
Microwave-assisted protein enzymatic digestion
- MS:
-
Mass spectrometry
- MS/MS:
-
Tandem mass spectrometry
- MW:
-
Molecular weight
- NA:
-
Not assigned
- PCT:
-
Pressure cycling technology
- RP:
-
Reversed phase
- TCEP:
-
Tris(2-carboxyethyl) phosphine
- TOF:
-
Time-of-flight
References
Aebersold, R., and Mann, M. (2003). Mass spectrometry-based proteomics. Nature 422, 198–207.
Blonder, J., Chan, K.C., Issaq, H.J., and Veenstra, T.D. (2006). Identification of membrane proteins from mammalian cell/tissue using methanol-facilitated solubilization and tryptic digestion coupled with 2D-LC-MS/MS. Nat Protoc 1, 2784–2790.
Boyne, M.T., Garcia, B.A., Li, M., Zamdborg, L., Wenger, C.D., Babai, S., and Kelleher, N.L. (2009). Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval. J Proteome Res 8, 374–379.
Cano, M.P., Hernandez, A., and DeAncos, B. (1997). High pressure and temperature effects on enzyme inactivation in strawberry and orange products. J Food Sci 62(1), 85–88.
Chomczynski, P., and Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156–159.
Domon, B., and Aebersold, R. (2006). Mass spectrometry and protein analysis. Science 312, 212–217.
Gross, V., Carlson, G., Kwan, A.T., Smejkal, G., Freeman, E., Ivanov, A.R., and Lazarev, A. (2008). Tissue fractionation by hydrostatic pressure cycling technology: the unified sample preparation technique for systems biology studies. J Biomol Tech 19, 189–199.
Hauser, N.J., and Basile, F. (2008). Online microwave D-cleavage LC-ESI-MS/MS of intact proteins: Site-specific cleavages at aspartic acid residues and disulfide bonds. J Proteome Res 7, 1012–1026.
Hauser, N.J., Han, H., McLuckey, S.A., and Basile, F. (2008). Electron transfer dissociation of peptides generated by microwave D-cleavage digestion of proteins. J Proteome Res 7, 1867–1872.
Havlis, J., Thomas, H., Sebela, M., and Shevchenko, A. (2003). Fast-response proteomics by accelerated in-gel digestion of proteins. Anal Chem 75, 1300–1306.
Hernandez, A., and Cano, M.P. (1998). High-pressure and temperature effects on enzyme inactivation in tomato puree. J Agric Food Chem 46, 266–270.
Hixson, K.K., Adkins, J.N., Baker, S.E., Moore, R.J., Chromy, B.A., Smith, R.D., McCutchen-Maloney, S.L., and Lipton, M.S. (2006). Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics. J Proteome Res 5, 3008–3017.
Isaacson, T., Damasceno, C.M., Saravanan, R.S., He, Y., Catala, C., Saladie, M., and Rose, J.K. (2006). Sample extraction techniques for enhanced proteomic analysis of plant tissues. Nat Protoc 1, 769–774.
Kim, B.C., Lopez-Ferrer, D., Lee, S.M., Ahn, H.K., Nair, S., Kim, S.H., Kim, B.S., Petritis, K., Camp, D.G., Grate, J.W., et al. (2009). Highly stable trypsin-aggregate coatings on polymer nanofibers for repeated protein digestion. Proteomics 9, 1893–1900.
Kiser, J.Z., Post, M., Wang, B., and Miyagi, M. (2009). Streptomyces erythraeus trypsin for proteomics applications. J Proteome Res 8, 1810–1817.
Lill, J.R., Ingle, E.S., Liu, P.S., Pham, V., and Sandoval, W.N. (2007). Microwave-assisted proteomics. Mass Spectrom Rev 26, 657–671.
Lopez-Ferrer, D., Capelo, J.L., and Vazquez, J. (2005). Ultra fast trypsin digestion of proteins by high intensity focused ultrasound. J Proteome Res 4, 1569–1574.
Lopez-Ferrer, D., Heibeck, T.H., Petritis, K., Hixson, K.K., Qian, W., Monroe, M.E., Mayampurath, A., Moore, R.J., Belov, M.E., Camp, D.G., 2nd, et al. (2008a). Rapid sample processing for LC-MS-based quantitative proteomics using high intensity focused ultrasound. J Proteome Res 7, 3860–3867.
Lopez-Ferrer, D., Hixson, K.K., Smallwood, H.S., Squier, T.C., Petritis, K., and Smith, R.D. (2009). Evaluation of a high-intensity focused ultrasound-immobilized trypsin digestion and 18O-labeling method for quantitative proteomics. Anal Chem 81, 6272–6277.
Lopez-Ferrer, D., Martinez-Bartolome, S., Villar, M., Campillos, M., Martin-Maroto, F., and Vazquez, J. (2004). Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST. Anal Chem 76, 6853–6860.
Lopez-Ferrer, D., Petritis, K., Hixson, K.K., Heibeck, T.H., Moore, R.J., Belov, M.E., Camp, D.G., 2nd, and Smith, R.D. (2008b). Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: Proteomics on the fly. J Proteome Res 7, 3276–3281.
Lopez-Ferrer, D., Petritis, K., Lourette, N.M., Clowers, B., Hixson, K.K., Heibeck, T., Prior, D.C., Pasa-Tolic, L., Camp, D.G., 2nd, Belov, M.E., et al. (2008c). On-line digestion system for protein characterization and proteome analysis. Anal Chem 80, 8930–8936.
Manza, L.L., Stamer, S.L., Ham, A.J., Codreanu, S.G., and Liebler, D.C. (2005). Sample preparation and digestion for proteomic analyses using spin filters. Proteomics 5, 1742–1745.
Pramanik, B.N., Mirza, U.A., Ing, Y.H., Liu, Y.H., Bartner, P.L., Weber, P.C., and Bose, A.K. (2002). Microwave-enhanced enzyme reaction for protein mapping by mass spectrometry: A new approach to protein digestion in minutes. Protein Sci 11, 2676–2687.
Qian, W.J., Liu, T., Petyuk, V.A., Gritsenko, M.A., Petritis, B.O., Polpitiya, A.D., Kaushal, A., Xiao, W., Finnerty, C.C., Jeschke, M.G., et al. (2009). Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled “universal” reference sample. J Proteome Res 8, 290–299.
Rial-Otero, R., Carreira, R.J., Cordeiro, F.M., Moro, A.J., Fernandes, L., Moura, I., and Capelo, J.L. (2007). Sonoreactor-based technology for fast high-throughput proteolytic digestion of proteins. J Proteome Res 6, 909–912.
Russell, W.K., Park, Z.Y., and Russell, D.H. (2001). Proteolysis in mixed organic-aqueous solvent systems: Applications for peptide mass mapping using mass spectrometry. Anal Chem 73, 2682–2685.
Sapan, C.V., Lundblad, R.L., and Price, N.C. (1999). Colorimetric protein assay techniques. Biotechnol Appl Biochem 29(Pt 2), 99–108.
Smejkal, G.B., Robinson, M.H., Lawrence, N.P., Tao, F., Saravis, C.A., and Schumacher, R.T. (2006). Increased protein yields from Escherichia coli using pressure-cycling technology. J Biomol Tech 17, 173–175.
Smejkal, G.B., Witzmann, F.A., Ringham, H., Small, D., Chase, S.F., Behnke, J., and Ting, E. (2007). Sample preparation for two-dimensional gel electrophoresis using pressure cycling technology. Anal Biochem 363, 309–311.
Swatkoski, S., Gutierrez, P., Ginter, J., Petrov, A., Dinman, J.D., Edwards, N., and Fenselau, C. (2007a). Integration of residue-specific acid cleavage into proteomic workflows. J Proteome Res 6, 4525–4527.
Swatkoski, S., Gutierrez, P., Wynne, C., Petrov, A., Dinman, J.D., Edwards, N., and Fenselau, C. (2008). Evaluation of microwave-accelerated residue-specific acid cleavage for proteomic applications. J Proteome Res 7, 579–586.
Swatkoski, S., Russell, S., Edwards, N., and Fenselau, C. (2007b). Analysis of a model virus using residue-specific chemical cleavage and MALDI-TOF mass spectrometry. Anal Chem 79, 654–658.
van Montfort, B.A., Doeven, M.K., Canas, B., Veenhoff, L.M., Poolman, B., and Robillard, G.T. (2002). Combined in-gel tryptic digestion and CNBr cleavage for the generation of peptide maps of an integral membrane protein with MALDI-TOF mass spectrometry. Biochim Biophys Acta 1555, 111–115.
Wang, H., Qian, W.J., Mottaz, H.M., Clauss, T.R., Anderson, D.J., Moore, R.J., Camp, D.G., 2nd, Khan, A.H., Sforza, D.M., Pallavicini, M., et al. (2005). Development and evaluation of a micro- and nanoscale proteomic sample preparation method. J Proteome Res 4, 2397–2403.
Washburn, M.P., Wolters, D., and Yates, J.R., 3rd (2001). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19, 242–247.
Wisniewski, J.R., Zougman, A., Nagaraj, N., and Mann, M. (2009). Universal sample preparation method for proteome analysis. Nat Methods 6, 359–362.
Wolters, D.A., Washburn, M.P., and Yates, J.R., 3rd (2001). An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73, 5683–5690.
Wu, C.C., MacCoss, M.J., Howell, K.E., and Yates, J.R., 3rd (2003). A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 21, 532–538.
Wu, C.C., and Yates, J.R., 3rd (2003). The application of mass spectrometry to membrane proteomics. Nat Biotechnol 21, 262–267.
Xiang, R., Shi, Y., Dillon, D.A., Negin, B., Horvath, C., and Wilkins, J.A. (2004). 2D LC/MS analysis of membrane proteins from breast cancer cell lines MCF7 and BT474. J Proteome Res 3, 1278–1283.
Zhong, H., Zhang, Y., Wen, Z., and Li, L. (2004). Protein sequencing by mass analysis of polypeptide ladders after controlled protein hydrolysis. Nat Biotechnol 22, 1291–1296.
Acknowledgments
Portions of this work were supported by the NIH National Center for Research Resources (NCRR, RR018522), NIH National Cancer Institute (R21 CA12619-01), and the Pacific Northwest National Laboratory’s (PNNL) Laboratory Directed Research and Development Program. This research was enabled in part by capabilities developed under support from the U.S. Department of Energy (DOE) Office of Biological and Environmental Research and the NCRR, and was conducted in the Environmental Molecular Sciences Laboratory, a DOE national scientific user facility located at the Pacific Northwest National Laboratory (PNNL) in Richland, WA. PNNL is a multiprogram national laboratory operated by Battelle for the DOE under Contract No. DE-AC05-76RLO 1830.
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Lopez-Ferrer, D., Hixson, K.K., Belov, M.E., Smith, R.D. (2011). Ultra-Fast Sample Preparation for High-Throughput Proteomics. In: Ivanov, A., Lazarev, A. (eds) Sample Preparation in Biological Mass Spectrometry. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0828-0_8
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DOI: https://doi.org/10.1007/978-94-007-0828-0_8
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