MTDB Creator
This software can be used to generate a Mass and Time tag database (Microsoft Access format) from local MS/MS search engine results from either SEQUEST or X!Tandem. This database can then act as input to VIPER and MultiAlign for matching high resolution LC-MS features to peptides.
The installer includes example data from Salmonella typhimurium in file ExampleDatabase.mdb. Note that the the X!Tandem results files need to be converted to tab-delimited format using the Peptide Hit Results Processor application prior to processing with the MTDB creator. In addition, SEQUEST result files need to be converted to a synopsis file (_syn.txt) using the Peptide File Extractor and then the _syn.txt file must be processed by the Peptide Hit Results Processor.
The "Data Extraction and Analysis for LC-MS Based Proteomics" sessions at the 2007 and 2008 US HUPO conferences discussed the use of the MTDB Creator to create AMT tag databases. PDF files of the slides presented are available for download as a 5 MB PDF file (2007) and a 6.5 MB PDF file (2008).
The methods embodied in this software to derive the Kangas/Petritis retention time prediction values are covered by U.S. patent 7,136,759 and pending patent 2005-0267688A1. The software is made available solely for non-commercial research purposes on an "as is" basis by Battelle Memorial Institute. If rights to deploy and distribute the code for commercial purposes are of interest, please e-mail Bruce Harrer.
| Download Software Tool |
| Version | v1.0.3488 | Requirements | Microsoft NET Framework 1.1 |
| Date Updated | July 20, 2009 | File Size (Software Tool) | 6.4 MB (ZIP) |
| Registration Required | No | File size (Source Code) | n/a |
| Developers | Deep Jaitly and Matthew Monroe | ||
| Comments |
This version now includes the Kanagas/Petritis retention time prediction algorithm. See also the complete Revision History |
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Acknowledgment
All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:
Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.