U.S. Department of Energy

Pacific Northwest National Laboratory

MTDB Creator

This software can be used to generate an Accurate Mass and Time tag database (Microsoft Access format) from local MS/MS search engine results from either SEQUEST or X!Tandem.

Area of Research: 
Description: 

The database can act as input to VIPER and MultiAlign for matching high resolution LC-MS features to peptides.

Example data files are available as a separate download, 101 MB (ZIP). This file contains an example Access database created using 8 quality assessment (QC_Shew) datasets from a Thermo Fisher Scientific LTQ-Orbitrap instrument, each analyzed by SEQUEST. Prior to loading into the MTDB Creator, the SEQUEST results were converted to the synopsis file(_syn.txt) format using the Peptide File Extractor. Then the _syn.txt file was processed by the Peptide Hit Results Processor to obtain several additional files.

Similarly, X!Tandem results files must be converted to a tab-delimited format using the Peptide Hit Results Processorapplication prior to processing with the MTDB creator.

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).

Downloads: 
AttachmentSize
Package icon MTDB Creator Installer15.01 MB
Package icon MTDB Creator Source Code4.09 MB

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, as shown in the Readme file for the given application or on the website that more fully describes the application.

 

Disclaimer

These programs are primarily designed to run on Windows machines. Please use them at your own risk. This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

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.

We would like your feedback about the usefulness of the tools and information provided by the Resource. Your suggestions on how to increase their value to you will be appreciated. Please e-mail any comments to proteomics@pnl.gov

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