Mass spectrometry database mining

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. 

Developments in mass spectrometry technology, together with the availability of extensive DNA and protein sequence databases and software tools for data mining, has made possible rapid and sensitive mass spectrometry-based procedures for protein identification. Two basic types of mass spectrometers are commonly used for this purpose Matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF) mass spectrometry (MS) and electrospray ionization (ESI)-MS. MALDI-TOF instruments are now quite common in biochemistry laboratories and are very simple to use, requiring no special training. ESI instruments, usually coupled to capillary/nanoLC systems, are more complex and require expert operators. We will therefore focus on the use of MALDI-... 

Figure 1 Schematic illustration of the proteomics process comprising the utilization of both gel-base and liquid-phase separations interphased to mass spectrometry analysis followed by database search mining, annotation, and a final link to the functional role of proteins.

The ProteinProspector Server (http //prospector.ucsf.edu) from the University of California San Francisco mass spectrometry facility. This suite of programs includes various tools for mining sequence databases in conjunction with mass spectrometry experiments, such as MS-Fit, MS-Tag, MS-Product and others. 

Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments ... 

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