4
D. R. GOODLETT et al.
Table 1.1. Comprehensive Proteome Projects
Organisms
References
Saccharomyces cerevisiae
Hodges, P.E., et al. Nucl. Acids Res. 1998, 26, 68-72.
Salmonella enterica
O'Connor, C. D. et al. Electrophoresis 1997, 18, 1483-1490.
Spiroplasma melliferum
Cordwell, S.J., et al. Electrophoresis 1997, 18, 1335-1346.
Mycobacterium tuberculosis
Urquhart, B.L., et al. Electrophoresis 1997, 18, 1384-1392.
Ochrobactrum anthropi
Wasinger, V.C., et al. Electrophoresis 1997, 18, 1373-1383.
Haemophilus influenza
Link, A. J:, et al. Electrophoresis 1997, 18, 1314-1334.
Synechocystis spp.
Sazukam T. & o. Ohara Electrophoresis, 1997, 18, 1252-1258.
Escherichia coli
van Bogelen, R. A., et al. Electrophoresis, 1997, 18, 1243-125l.
Rhizobium leguminosarum
Guerreiro, N. et aI., Mol. Plant Microbe Interact., 1997, 10,
506-516.
Dictyostelium discoideum
Yan, J. X., et al. Electrophoresis 1997, 18, 491-497.
Tissues
References
Human bladder squamous call
Celis, J. et al., FEBS Lett. 1996, 398, 129-134.
carcinoma, Human keratinocytes,
Human fubroblasts, Mouse kidney
Human liver & plasma
Appel, R.D., et al. Electrophoresis 1993.
Rat serum
Haynes, P., et aI., Electrophoresis 1998, 19, 1484-1492.
As listed in Table 1.1 numerous proteome projects are underway for both
whole organisms and specific cell types. In contrast to genome sequencing where
numerous prokaryotic and two eukaryotic genomes have been described (Goffeau, et al. 1996; Fleischmann, et al. 1995; Fraser, et al. 1997) none of the listed
proteome projects is approaching completion. Difficulties which have prevented
completion of proteome projects include:
1) an inability to amplify protein sequences as can be done with nucleic acid
sequences,
2) post-translational modifications that in the case of regulatory proteins may be
non-stoichiometric and
3) the presence of isoforms as in the case of glycoproteins.
Additional complications in proteome analysis that are more difficult to address
arise because of the dynamic nature of proteomes and the variation in physicochemical properties between proteins such as pI, solubility and size. A single
genome can, because of variations in cell cycle, state of differentiation or nutrient
supply, give rise to different proteomes. In order to prepare reproducibly the
same proteome for characterization all parameters affecting cell growth and the
purification process must be controlled.
In this chapter we will present various aspects of basic proteome analysis and
describe methods employed for protein characterization on a large scale as well
D. R. GOODLETT et al.
Table 1.1. Comprehensive Proteome Projects
Organisms
References
Saccharomyces cerevisiae
Hodges, P.E., et al. Nucl. Acids Res. 1998, 26, 68-72.
Salmonella enterica
O'Connor, C. D. et al. Electrophoresis 1997, 18, 1483-1490.
Spiroplasma melliferum
Cordwell, S.J., et al. Electrophoresis 1997, 18, 1335-1346.
Mycobacterium tuberculosis
Urquhart, B.L., et al. Electrophoresis 1997, 18, 1384-1392.
Ochrobactrum anthropi
Wasinger, V.C., et al. Electrophoresis 1997, 18, 1373-1383.
Haemophilus influenza
Link, A. J:, et al. Electrophoresis 1997, 18, 1314-1334.
Synechocystis spp.
Sazukam T. & o. Ohara Electrophoresis, 1997, 18, 1252-1258.
Escherichia coli
van Bogelen, R. A., et al. Electrophoresis, 1997, 18, 1243-125l.
Rhizobium leguminosarum
Guerreiro, N. et aI., Mol. Plant Microbe Interact., 1997, 10,
506-516.
Dictyostelium discoideum
Yan, J. X., et al. Electrophoresis 1997, 18, 491-497.
Tissues
References
Human bladder squamous call
Celis, J. et al., FEBS Lett. 1996, 398, 129-134.
carcinoma, Human keratinocytes,
Human fubroblasts, Mouse kidney
Human liver & plasma
Appel, R.D., et al. Electrophoresis 1993.
Rat serum
Haynes, P., et aI., Electrophoresis 1998, 19, 1484-1492.
As listed in Table 1.1 numerous proteome projects are underway for both
whole organisms and specific cell types. In contrast to genome sequencing where
numerous prokaryotic and two eukaryotic genomes have been described (Goffeau, et al. 1996; Fleischmann, et al. 1995; Fraser, et al. 1997) none of the listed
proteome projects is approaching completion. Difficulties which have prevented
completion of proteome projects include:
1) an inability to amplify protein sequences as can be done with nucleic acid
sequences,
2) post-translational modifications that in the case of regulatory proteins may be
non-stoichiometric and
3) the presence of isoforms as in the case of glycoproteins.
Additional complications in proteome analysis that are more difficult to address
arise because of the dynamic nature of proteomes and the variation in physicochemical properties between proteins such as pI, solubility and size. A single
genome can, because of variations in cell cycle, state of differentiation or nutrient
supply, give rise to different proteomes. In order to prepare reproducibly the
same proteome for characterization all parameters affecting cell growth and the
purification process must be controlled.
In this chapter we will present various aspects of basic proteome analysis and
describe methods employed for protein characterization on a large scale as well