Protein, profiling

Crawford, D. J. 1976. Variation in seed protein profiles of Chenopodium fremontii. Biochem. Syst. Ecol. 4 169-172. 

Adjunctive to flux control analysis, other components of metabolism that contribute to product accumulation are needed including (1) substrate/precursor pool sizes (metabolomics), (2) co-factor capacities (metabolomics), (3) gene expression profiles (transcriptomics and quanfifafive real-time PCR), (4) protein profiles (pro-... 

The dialysed sample was fractionated by cation exchange chromatography. A 40-50 ml sample was applied to a CM-Sepharose CL-6B column (1.5 x 15 cm). Unbound proteins were removed with 50 mM MES pH 6.8, 1 mM DTT, and the bound proteins were eluted with an increasing NaCl gradient from 0 - 0.4 M NaCl in a total volume of 500 ml. The flow was 25 ml/h and fractions of 8.33 ml were collected. The protein profile was measured at 280 nm. 

Rockabrand, D. Austin, T. Kaiser, R. Blum, P Bacterial growth state distinguished by single-cell protein profiling Does chlorination kill coliforms in municipal effluent Appl. Environ. Microbiol. 1999,65,4181-4188. 

Cain,T. Lubman, D. Weber, W. J. Differentiation of bacteria using protein profiles from matrix assisted laser desorption/ionization time of flight mass spectrometry. Rapid Comm. Mass Spectrom. 1994,8,1026-1030. 

Holland et al. proposed a simpler and faster approach using the protein profile obtained directly from whole cells rather than from cellular extracts or affinity beads.17 This was the first report of the whole-cell MALDI-TOF MS... 

Fortunately these unforeseen variables did not affect the most abundant peaks, nor the correct identification of the blind-coded bacteria. While differences associated with matrix and instrumental parameters were expected, the authors conducting this experiment did not anticipate the extent and speed with which bacteria could respond, through their protein profiles, to subtle environmental changes. 

Dickinson, D. N. Due, M. T. L. Haskins, W. E. Gornushkin, I. Winefordner, J. D. Powell, D. H. Venkateswaran, K. Species differention of a diverse suite of Bacillus spores by mass spectrometry-based protein profiling. Appl. Environ. Microbiol. 2004,70,475 482. 

For these reasons we have developed a different approach that measures differential expression of intact proteins.21 In this approach the proteins are extracted from the cell, separated on an HPLC column, ionized via electrospray, and automatically deconvoluted into their respective uncharged nominal masses. By this methodology it is then possible to obtain accurate, intact protein profiles of the individual strains of bacteria. Because the masses of the detected proteins are accurate to +2 Da from run to run, it is possible to subtract protein profiles from known strains to quickly identify differences in protein expression among newly mutated strains. 

Variations on the spectral peaks from different species of the same genus were also observed. Three species of Pseudomonas produced the spectra shown in Figure 14.2. These spectra are clearly unique and were used to correctly identify unknown samples. Because of peak ratio reproducibility issues in bacterial protein profiles obtained by MALDI MS,11 a fingerprint approach that had been used for other mass spectrometry approaches has not been used. The profile reproducibility problem was first recognized by Reilly et al.12,13 and later researched by others in the field.14,15 As a later alternative, a direct comparison of the mass-to-charge ratio (m/z) of the unknown mass spectral peaks with a database of known protein masses has been used to identify unknown samples.14... 

An example of the microorganism differentiation power achievable with the protein profiling approach is illustrated using the MALDI mass spectra of Escherichia coli and Cryptosporidium parvum (Figure 14.3). Clear... 

D Liquid Mass Mapping of Tumor Cell Line Secreted Samples, Application to Metastasis-Associated Protein Profiles... 

Zhou, F., Johnston, M. V. (2005). Protein profiling by capillary isoelectric focusing, reversed phase liquid chromatography, and mass spectrometry. Electrophoresis 26(7-8), 1383-1388. 

Von Haller, P.D., Yi, E., Donohoe, S., Vaughn, K., Keller, A., Nesvizhskii, A.I., Eng, J., Li, X.J., Goodlett, D.R., Aebersold, R., Watts, J.D. (2003). The Application of New Software Tools to Quantitative Protein Profiling Via Isotope-coded Affinity Tag (ICAT) and Tandem Mass Spectrometry II. Evaluation of Tandem Mass Spectrometry Methodologies for Large-Scale Protein Analysis, and the Application of Statistical Tools for Data Analysis and Interpretation. Mol. Cell. Proteomics 2, 428 -42. 

Taoka M et al. Protein profiling of rat cerebella during development. Electrophoresis 2000 21 1872-1879. 

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