Summary
Prokaryotic protein expression changes in detectable amounts due to the environmental stimuli encountered by the organism. To understand the underlying mechanisms involved it is necessary to comprehensively detect both the proteins present and their relative abundance under the growth conditions of interest. LC-MS based accurate mass and time (AMT) tag method along with the use of clustering software can provide a visual and more comprehensive understanding of significant protein abundance increases and decreases. These data then can be effectively used to pin-point proteins of interest for further genetic and physiological studies. This method allows for the identification and quantitation of thousands of proteins in a single mass spectrometric analysis and is more comprehensive than two dimensional electrophoresis and shotgun approaches.
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References
Adkins, J.N. et al. (2006) Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions. Mol Cell Proteomics 5, 1450–1461.
Logan, B.E. & Regan, J.M. (2006) Electricity-producing bacterial communities in microbial fuel cells. Trends Microbiol 14, 512–518.
Hunter, E.M., Mills, H.J. & Kostka, J.E. (2006) Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments. Appl Environ Microbiol 72, 5689–5701.
van der Heijden, M.G. et al. (2006) Symbiotic bacteria as a determinant of plant community structure and plant productivity in dune grassland. FEMS Microbiol Ecol 56, 178–187.
Zimmer, J.S., Monroe, M.E., Qian, W.J. & Smith, R.D. (2006) Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom Rev 25, 450–482.
Pasa-Tolic, L., Masselon, C., Barry, R.C., Shen, Y.&Smith, R.D. (2004) Proteomic analyses using an accurate mass and time tag strategy. Biotechniques 37, 621–624, 626–633, 636 passim.
Callister, S.J. et al. (2006) Application of the accurate mass and time tag approach to the proteome analysis of sub-cellular fractions obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and photo-synthetic cell cultures. J Proteome Res 5, 1940–1947.
Fang, R. et al. (2006) Differential label- free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach. Mol Cell Proteomics 5, 714–725.
Umar, A., Luider, T.M., Foekens, J.A. & Pasa-Tolic, L. (2006) NanoLC-FT-ICR MS improves proteome coverage attainable for 3000 laser-microdissected breast carcinoma cells. Proteomics 7, 323–329.
Resch, W., Hixson, K.K., Moore, R.J., Lipton, M.S.&Moss, B. (2006) Protein composition of the vaccinia virus mature virion. Virology 358, 233–247.
Shi, L. et al. (2006) Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages. J Biol Chem 281, 29131–29140.
Qian, W.J. et al. (2005) Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach. Mol Cell Proteomics 4, 700–709.
Bogdanov, B. & Smith, R.D. (2005) Proteomics by FTICR mass spectrometry: top down and bottom up. Mass Spectrom Rev 24, 168–200.
Eng, J.K., McCormack, A.L. & Yates, J.R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5, 976–989.
Perkins, D.N., Pappin, D.J., Creasy, D.M. & Cottrell, J.S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567.
Hixson, K.K. et al. (2006) Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics. J Proteome Res 5, 3008–3017.
Ding, Y.H. et al. (2006) The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions. Biochim Biophys Acta 1764, 1198–1206.
Callister, S.J. et al. (2006) Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J Proteome Res 5, 277–286.
Kelly, R.T. et al. (2006) Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrom-etry. Anal Chem 78, 7796–7801.
Shen, Y. et al. (2001) Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics. Anal Chem 73, 1766–1775.
Jaitly, N. et al. (2006) Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline. Anal Chem 78, 7397–7409.
Fujiki, Y., Hubbard, A.L., Fowler, S. & Lazarow, P.B. (1982) Isolation of intracellu-lar membranes by means of sodium carbonate treatment: application to endoplasmic reticulum. J Cell Biol 93, 97–102.
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Hixson, K.K. (2009). Label-Free Relative Quantitation of Prokaryotic Proteomes Using the Accurate Mass and Time Tag Approach. In: Lipton, M.S., Paša-Tolic, L. (eds) Mass Spectrometry of Proteins and Peptides. Methods In Molecular Biology, vol 492. Humana Press. https://doi.org/10.1007/978-1-59745-493-3_3
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DOI: https://doi.org/10.1007/978-1-59745-493-3_3
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