Proteins mass spectrometry and

Protein Mass Spectrometry and Functional Proteomics Group, Rudolf-Virchow-Center for Experimental Biomedicine, University of Wuerzburg, Wuerzburg, Germany. 

The basic class definitions and other infrastructure are provided in the Biobase package. The base class is the eSet and it has places to store assay data, phenotypic information, and data about the features that were measured and about the experiment that was performed to collect these data. This basic class can then be extended in many different ways, specializing in some of the inputs, and in some cases adding new slots that are relevant to a specific type of experiment. The eSet class has been extended to support expression data, SNP data, and genomic annotation. For expression data the ExpressionSet class has been defined, and it too is quite general. The class can be used for any sort of expression (and is in no way restricted to microarray experiments for mRNA expression, although that is where it is used most). Similar data structures have been used for representing data from experiments in protein mass spectrometry and flow cytometry. 

Kaddis, C. S. Loo, J. A. Native protein mass spectrometry and ion mobiUty ESI and large flying proteins. Anal. Chem. 2007, 79, 1779-1784. 

Domon B, Aebersold R (2006) Mass spectrometry and protein analysis. Science 312 212-217... 

Figure 5.11. Generic approaches to identify interacting proteins within complexes. The complex is isolated from cells by affinity purification using a tag sequence attached to a protein known to be in the complex. Alternatively, the complex can be immunprecipitated with an antibody to one of the proteins in the complex. The proteins are resolved by polyacrylamide gel electrophoresis, proteolyzed, and the mass of the resulting peptides is determined by mass spectrometry. Alternatively, the proteins can be proteolyzed and the resulting peptides resolved by liquid chromatography. The peptide masses are then determined by mass spectrometry and used for database searching to identify the component proteins.

Gauss, C., Kalkum, M., Lowe, M., Lehrach, H., and Klose, J. (1999). Analysis of the mouse proteome. (I) Brain proteins Separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation. Electrophoresis 20, 575-600. 

Neubauer, G., King, A., Rappsilber, J., Calvio, C., Watson, M., Ajuh, P., Sleeman, J., Lamond, A., and Mann, M. (1998). Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nat. Genet. 20, 46-50. 

Goodacre, R. Karim, A. Kaderbhai, M. A. Kell, D. B. Rapid and quantitative analysis of recombinant protein expression using pyrolysis mass spectrometry and artificial neural networks Application to mammalian cytochrome b5 in Escherichia coli. J. Biotechnol. 1994,34,185-193. 

Demirev, P. A. Ho, Y. P. Ryzhov, V. Fenselau, C. Microorganism identification by mass spectrometry and protein database searches. Anal. Chem. 1999, 71, 2732-2738. 

Pineda, F. J. Antoine, M. D. Demirev, P A. Feldman, A. B. Jackman, J. Longenecker, M. Lin, J. S. Microorganism identification by matrix-assisted laser/desorption ionization mass spectrometry and model-derived ribosomal protein biomarkers. Anal. Chem. 2003,75,3817-3822. 

McGovern, A. C. Ernill, R. Kara, B. V. Kell, D. B. Goodacre, R. Rapid analysis of the expression of heterologous proteins in Escherichia coli using pyrolysis mass spectrometry and Fourier transform infrared spectroscopy with chemometrics Application to a2- interferon production. J. Biotechnol. 1999, 72,157-167. 

Qian, W.J., Liu, T., Monroe, M.E., Strittmatter, E.F., Jacobs, J.M., Kangas, L.J., Petritis, K., Camp, D.G., 2nd, Smith, R.D. (2005b). Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis the human proteome. J. Proteome Res. 4, 53-62. 

The ability to resolve and characterize complicated protein mixtures by the combination of 2DLC and online mass spectrometry permits the combination of sample fractionation/simplification, top-down protein mass information, and bottom-up peptide level studies. In our lab, the simplified fractions generated by 2D(IEX-RP)LC are digested and analyzed using common peptide-level analysis approaches, including peptide mass fingerprinting (Henzel et al., 1993 Mann et al., 1993), matrix-assisted laser desorption/ionization (MALDI) QTOF MS/MS (Millea et al., 2006), and various capillary LC/MS/MS methodologies (e.g., Ducret et al., 1998). 

Huber, C.G., Premstaller, A. (1999). Evaluation of volatile eluents and electrolytes for high-performance liquid chromatography-electrospray ionization mass spectrometry and capillary electrophoresis-electrospray ionization mass spectrometry of proteins. I. Liquid chromatography. J. Chromatogr. A 849, 161-173. 

Analysis, Fate and Removal of Pharmaceuticals in the Water Cycle Food Contaminants and Residue Analysis Protein Mass Spectrometry... 

Joubert-Caron R et al. Protein analysis by mass spectrometry and sequence database searching a proteomic approach to identify human lymphoblastoid cell line proteins. Electrophoresis 2000 21 2566— 2575. 

However, IHC as a practical method continues to evolve with increasing demands for standardization, and for true quantification of protein analytes by weight, in the context of their cellular microenvironment. Further studies combining proteomics by mass spectrometry and IHC are likely to lead to the refinement of both methods in the analysis of FFPE tissues. The end result may be the creation of a broader field that defines and quantifies protein expression at a cellular level, incorporating the advantages of the wide spectrum of proteins demonstrable by mass spectrometry and the precise localization offered by IHC. 

The techniques developed to study protein interactions can be divided into a number of major categories (Table 31.1), including bioconjugation, protein interaction mapping, affinity capture, two-hybrid techniques, protein probing, and instrumental analysis (i.e., NMR, crystallography, mass spectrometry, and surface plasmon resonance). Many of these methods are dependent on the use of an initial bioconjugation step to discern key information on protein interaction partners. 

Stahl, N., Baldwin, M. A., Teplow, D. B., Hood, L., Gibson, B. W., Burlingame, A. L., and Prusiner, S. B. (1993). Structural studies of the scrapie prion protein using mass spectrometry and amino acid sequencing. Biochemistry 32, 1991-2002. 

Fig. 7. Protein identification with electrospray tandem mass spectrometry and a triple quadrupole mass spectrometer. Fragment spectra of several peptides are generated during one investigation. From the fragment spectra short sequence stretches can be read. Together with their mass location in the peptide of the measured mass, they can be used to specifically identify a protein in the database. Because the protein identification depends only on one peptide, several proteins can be identified from one sample.

For accurate determination of protein molecular weight, mass spectrometry and LC-MS have largely displaced SDS-PAGE. However, SDS-PAGE will still be used where estimates of molecular weight suffice or where MS instrument time is limited. 

McGovern et al.26 analyzed the expression of heterologous proteins in E. coli via pyrolysis mass spectrometry and FT-IR. The application was to a2-interferon production. To analyze the data, artificial neural networks (ANN) and PLS were utilized. Because cell pastes contain more mass than the supernatant, these were used for quantitative analyses. Both the MS and IR data were difficult to interpret, but the chemometrics used allowed researchers to gain some knowledge of the process. The authors show graphics indicating the ability to follow production via either technique. 

Figeys, D., Lock, C., Taylor, L., and Aebersold, R. (1998). Microfabricated device coupled with an electrospray ionization quadrupole time-of-flight mass spectrometer protein identifications based on enhanced-resolution mass spectrometry and tandem mass spectrometry data. Rapid Commun. Mass Spectrom. 12, 1435 — 1444. 

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