Protein mass spectrometry

Figure 2.4. Peptide fingerprinting by MALDI-TOF mass Spectrometry. Proteins are extracted and separated on by 2D gel electrophoresis. A spot of interest is excised from the gel, digested with trypsin, and ionized by MALDI. The precise mass of proteolytic fragments is determined by time-of- flight mass spectrometry. The identity of the protein is determined by comparing the peptide masses with a list of peptide masses generated by a simulated digestion of all of the open reading frames of the organism.

Ducret, A., Van Oostveen, I., Eng, J.K., Yates, J.R., 3rd, Aebersold, R. (1998). High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry. Protein Sci. 7, 706-719. 

Jacobsen, R.B., Sale, K.L., Ayson, M.J., Novak, P., Hong, J., Lane, P., Wood, N.L., Kruppa, G.H., Young, M.M., and Schoeniger, J.S. (2006) Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry. Protein Sci. 15, 1303-1317. 

J. J. Lennon and K. A. Walsh. Locating and Identifying Posttranslational Modifications by In-Source Decay During MALDI-TOF Mass Spectrometry. Protein Sci., 8(1999) 2487-2493. 

Proteins fall into three classes when characterized with mass spectrometry proteins whose complete sequence is given in a database, proteins whose sequence is partially represented in expressed sequence tag databases, and proteins whose sequence is unknown. Proteins of the first class can be identified by peptide mass mapping in a very high through-... 

The application of electrospray ionization (ESI) to macromolecules was first described by Yamashita and Fenn in 1984, and he later applied this technique to the study of proteins in 1988. In ESI, charged droplets of protein were produced and the solvent was stripped away, leaving only the free protein ion. In 1987, Tanaka demonstrated that laser pnlses from a low-energy nitrogen laser could be used to ionize proteins from a surface. As described in a paper presented during the Second Japan-China Joint Symposium on Mass Spectrometry, proteins are desorbed from a glycerol matrix containing cobalt powder. The cobalt powder was necessary to increase absorption of the laser photons. ... 

Wendt, H., Durr, E., Thomas, R. M., Przybylski, M., and Bosshard, H. R. (1995). Characterization of leucine zipper complexes by electrospray ionization mass spectrometry. Protein ScL, 4, 1563-70. 

S. A. Carr, M. J. Huddleston, and M. F. Bean, Selective identification and differentiation of N- and O-linked oligosaccharides in glycoproteins by liquid chromatography-mass spectrometry, Protein Sci., 2 (1993) 183-196. 

Aebersold, R. Bures, E. J. Namchuk, M. Goghari, M. H. Shushan, B. Covey, T. C. 1992. Design, synthesis, and characterization of a protein sequencing reagent yielding amino acid derivatives with enhanced detectability by mass spectrometry. Protein Sci., 1,494-503. 

Gorman JJ, Ferguson BL, Speelman D, Mills D (1997) Determination of the disulfide bond arrangement of human respiratory syncytial virus attachment (G) protein by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Protein Sci 6 1380... 

Wang L, Lane LC, Smith DL (2001) Detecting structural changes in viral capsids by hydrogen exchange and mass spectrometry. Protein Sci 10 1234-1243... 

A. Tsarbopoulos, B. N. Pramanik, J. Labdon, P. Reichert, G. Gitlin, S. Patel, V. Sardana, T. L. Nagabhushan, and P. P. Trotta, Isolation and characterization of a resistant core peptide of recombinant human granulocyte-macrophage colony-stimulating factor (GM-CSF) confirmation of the GM-CSF amino acid sequence by mass spectrometry. Protein Sci. 2 (1993), 1948-1958. 

Surface-enhanced laser/desorption ionization mass spectrometry Protein-Chip . See Tang, N., Tomatore, P, and Weinberger, S.R., Current developments in SELDI affinity technology. Mass Spectrom. Rev. 23a, 34-44,2004. 

Protein Sequencing Mass Spectrometry Proteins were sequenced on an Applied Biosystems 477A protein sequencer. Polypeptide molecular weights were determined after analysis by a Sciex API-Ill electrospray ioniziation mass spectrometer. 

Hyperlinks to other mass spectrometry, protein chemistry, or molecular biology sites. 

Includes structural biology, mass spectrometry, protein arrays, bioinformatics, high throughput screening (HTS) assays, protein chemistry, cell biology, signal transduction, and physiology, as related to functional and structural proteomics and methods papers. 

Mass Spectrometry Protein Identification Internet Sites... 

We see two major appearing frontiers for new kinds of molecular data. The first is proteomics (See Chapter 4 of volume 2) and metabolomics. With a combination of 2D gel, mass spectrometry, protein microarray and yeast-two-hybrid methods, a large amount of protein sequence, expression, and interaction data will be produced on a cell-wide level. On the one hand, bioinformatics has to address the challenge of interpreting these data. On the other hand, especially the protein interaction data will provide an interesting basis for probing deeper into the details of regulatory networks. Such data are collected in special protein interaction databases such as DIP [9,10] and BIND [11],... 

Cohen, S.L., Ferrd-DAmard, A.R., Burley, S.K. and Chait, B.T. (1995). Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Sci. 4, 1088-1099. 

Ge, Y Lawhorn, B.G. Elnaggar, M. Sze, S.K. Begley, T.P. McLafferty, F.W. Detection of four oxidation sites in viral prolyl-4-hydroxylase hy top-down mass spectrometry. Protein Science 2003,12, 2320-2326. 

Wagner, D.S., Melton, L.G., Yan, Y., et al. (1994) Deuterium exchange of alpha-helices and beta-sheets as monitored by electrospray ionization mass spectrometry. Protein Sci, 3 (8), 1305-1314. 

Akashi, S., Takio, K (2000) Characterization of the interface structure of enzyme-inhibitor complex by using hydrogen-deuterium exchange and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Protein Sci, 9 (12), 2497-2505. 

Waring, A.J., Mobley, P.W., Gordon, L.M. (1998) Conformational mapping of a viral fusion peptide in structure-promoting solvents using circular dichroism and electrospray mass spectrometry. Proteins 2 (Suppl), 38- 9. 

Burkitt, W., Domann, R, O Connor, G. (2010) Conformational changes in oxidatively stressed monoclonal antibodies studied by hydrogen exchange mass spectrometry. Protein Sci, 19 (4), 826-835. 

Loo, R.R., Dales, N., Andrews, RC. (1994) Surfactant effects on protein structure examined by electrospray ionization mass spectrometry. Protein Science, 3(11), 1975-1983. 

Sharma, S., Zheng, H., Huang, Y.J., et al. (2009) Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry. Proteins, 76 (4), 882-894. 

L. N. Amankawa, K. Harder, F. Jirik, and R. Aebersold, High-sensitivity determination of tyrosine phosphorylated peptides by on-line enzyme reactor and electrospray ionization mass spectrometry. Protein Sci. 4, 113-125 (1995). 

J. Zaia, D. Fabris, et al.. Monitoring metal ion flnx in reactions of metallothionein and drug-modified metallothionein by electrospray mass spectrometry, Protein Sci. 7, 2398-2404 (1998). 

Lennon JJ and Walsh KA (1999) Locating and identifying posttranslational modifications by in-source decay during MALDI-TOF mass spectrometry. Protein Science 8 2487-2493. 

---