Mass Spectrometry Databases

The package uses fragment as well as neutral loss searching yielding hit lists useful for determining possible chemical structures for an unknown compound even when the compound is clearly not in the reference database. A limit of 500 spectra from the users own mass spectrometry database is currently in place for the basic package but this can be overcome with an upgrade. 

S. R. Heller, Mass Spectrometry Databases and Search Systems, in Computer Supported Spectroscopic Databases, ed. 

Kapp, E.A. Schiitz, R Reid, G.E. Eddes, J.S. Moritz, R.L. O Hair, R.A.J. Speed, T.R Simpson, R.J. Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal. Chem. 2003, 75, 6251-6264. 

Murugaiyan, J., Ahrholdt, J Kowbel, V and Roesler, U. (2012) Establishment of a matrix-assisted laser desorption ionization time-of-flight mass spectrometry database for rapid identification of infectious achlorophyllous green micro-algae of the genus Prototheca. Clin. Microbiol Infect., 18, 461-467. 

Discuss the role of mass spectrometry databases in the identification of (a) known and (b) unknown compounds. 

JICST/JOIS. The Japan Information Center for Science and Technology (fICST) Mass Spectral Database is accessible to users in Japan through the JICST Eactual Database System (fOlS-E). The database uses the NIST/EPA/ MSCD data collection supplemented by spectra from the Mass Spectrometry Society of Japan (84). 

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

Figure 2.6. LC-tandem mass spectrometry to examine complex mixtures. The mixture of many different proteins is digested to yield peptides and the peptides are resolved into fractions hy cation exchange chromatography followed by reverse phase chromatography. The fractionation steps resolve the peptides into fractions that he processed hy tandem mass spectrometry to yield sequence information suitable for database searching.

Figure 3.1. Protein expression mapping using 2-D electrophoresis and mass spectrometry. The purpose is to compare protein expression patterns between cell types or in the same cell type under different growth conditions. Proteins are extracted from the different cell types and separated by 2D gel electrophoresis. Image analysis programs are used to compare the spot intensities between gels and identify proteins that are differentially expressed. The protein of interest is excised from the gel and its identity is determined by mass spectrometry. The power of the method increases greatly if the identity of a large number of proteins on the gel is known and present in a database because information can then be obtained without further mass spectrometry.

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.

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. 

Pineda, F. J. Lin, J. S. Fenselau, C. Dimerov, P. A. Testing the significance of microorganism identification by mass spectrometry and proteome database search. Anal. Chem. 2000, 72, 3739-3744. 

Dworzanski, J. R Snyder, A. P. Chen, R. Zhang, H. Wishart, D. Li, L. Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring. Anal. Chem. 2004,76,2355-2366. 

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