Abstract
Research in proteomics has created two significant needs: the need for an accurate public database of empirically derived mass spectrum information and the need for managing the I/O and organization of mass spectrometry data in the form of files and structures. Lack of an empirically derived database limits the ability of proteomic researchers to identify and study proteins. Managing the I/O and organization of mass spectrometry data is often time-consuming due to the many fields that need to be set and retrieved. As a result, incompatibilities and inefficiencies are created by each programmer handling this in his or her own way. Until recently, storage space and computing power has been the limiting factor in developing tools to handle the vast amount of mass spectrometry information. Now the resources are available to store, organize, and analyze mass spectrometry information.The Illinois Bio-Grid Mass Spectrometry Database is a database of empirically derived tandem mass spectra of peptides created to provide researchers with an organized and searchable database of curated spectrum information to allow more accurate protein identification. The Mass Spectrometry I/O Project creates a framework that handles mass spectrometry data I/O and data organization, allowing researchers to concentrate on data analysis rather than I/O. In addition, the Mass Spectrometry I/O Project leverages several cross-platform and portability-enhancing technologies, allowing it to be utilized on a variety of hardware and operating systems.
- {1} Beazley, David M. Tcl and SWIG as a C/C++ Development Tool. Department of Computer Science,University of Chicago. 1998.Google Scholar
- {2} Drew, Kevin; Angulo, David; Schilling, Alex; Freeman, Tim. Mass Spectra Analysis on the Illinois Biogrid. Proceedings of 2004 Midwest Software Engineering Conference, Chicago. June 2004. (Poster). (Electronically published http://facweb.cs.depaul.edu/bioinformatics/publications/MSEC-MassSpec-Poster 2004.ppt).Google Scholar
- {3} Eng, Jimmy K.; McCormack, Ashley L.; Yates III, John R. An Approach To Correlate Tandem Mass Spectral Data Of Peptides With Amino Acid Sequences In A Protein Database. J Am Soc Mass Spectrum, 1994, Number 4, pages 976-989.Google Scholar
- {4} Web address: http://www.genwaybio.com/. Last accessed August 18, 2005.Google Scholar
- {5} Kinter, M., Sherman, N. E. Protein Sequencing and Identification Using Mass Spectrometry. Wiley-Interscience, N.Y., 2000.Google Scholar
- {6} Ma, Bin; Zhang, Kaizhong; Hendrie, Christopher; Liang, Chengzhi; Li, Ming; Doherty-Kirby, Amanda; Lajoie, Gilles. PEAKS: Powerful Software For Peptide De Novo Sequencing By Tandem Mass Spectrometry. Rapid Communications in Mass Spectrometry, 2003, Num. 17, page 2337.Google Scholar
- {7} Pedrioli, Patrick G. A common open representation of mass spectrometry data and its application to proteomics research. Nature Biotechnology. Volume 22, issue 11, pages 81-92, November 2004.Google Scholar
- {8} Web address: http://www.peptideatlas.org. Last accessed August 18, 2005.Google Scholar
- {9} Perkins, DN; Pappin, DJ; Creasy, DM; and Cottrell, JS. Probability-based Protein Identification By Searching Sequence Databases Using Mass Spectrometry Data. Electrophoresis, 1999, Vol. 20, Num. 18, page 3551.Google Scholar
- {10} Prince, John T.; Carlson, Mark W.; Wang, Rong; Lu, Peng; Marcotte, Edward M. The Need For A Public Proteomics Repository. Nature Biotechnology, April 2004, Volume 22, Number 4, page 471.Google Scholar
- {11} Web address: http://www.proteomecommons.org/archive/1122567790437/index.html. Last accessed August 18, 2005.Google Scholar
- {12} Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Developing a Distributed and Scalable Foundation for Mass Spectrometry Data. DePaul University CTI Tech Report, pages 1-7. April 2005.Google Scholar
- {13} Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Comparing Mass Spectra. DePaul University CTI Tech Report, pages 1-7. March 2006.Google Scholar
- {14} Taylor, Alex J.; Johnson, Richard S. Sequence Database Searches Via De Novo Peptide Sequencing By Tandem Mass Spectrometry. Rapid Communications in Mass Spectrometry, 1997, Volume 11, pages 1067-1075.Google Scholar
- {15} Van Puymbrouck, Jennifer; Angulo, David; Battre, Dominic; Drew, Kevin; Hollenbeck, LeeAnn; Jabon, David; Schilling, Alex; von Laszewski, Gregor. A Batch Import Module for an Empirically Derived Mass Spectral Database. DePaul University CTI Tech Report, March 2006.Google Scholar
- {16} Wan, Katty X, Vidavsky, Ilan, and Gross, Michael L. Comparing Similar Spectra: From Similarity Index to Spectral Contrast Angle.Google Scholar
Index Terms
- Achieving I/O improvements in a mass spectral database
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