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Efficient analysis and extraction of MS/MS result data from Mascot result files
Florian Grosse-Coosmann1, Andreas M Boehm, Albert Sickmann
1Protein Mass Spectrometry and Functional Proteomics Group, Rudolf-Virchow-Center for Experimental Biomedicine, Universitaet Wuerzburg, Versbacher Strasse 9, D-97078 Wuerzburg, Germany. florian.coosmann@virchow.uni-wuerzburg.de
BMC Bioinformatics
|December 13, 2005
Summary
A new open-source program, mres2x, efficiently converts Mascot result files into a database-compatible format. This enables high-performance data analysis and complex querying for large shotgun proteomics datasets.
Area of Science:
- Proteomics
- Bioinformatics
- Computational Biology
Background:
- Mascot is a widely used tool for protein identification from MS/MS data.
- Analyzing large shotgun proteomics datasets with Mascot can strain computing resources.
- Existing solutions for Mascot data conversion lack open-source availability and database compatibility.
Purpose of the Study:
- To develop an open-source application for converting Mascot result files.
- To facilitate efficient handling and analysis of large proteomics datasets.
- To enable direct import of Mascot data into relational database management systems.
Main Methods:
- The mres2x program reads and analyzes Mascot result files.
- It extracts selected or all information into various output formats.
- Tabular output is optimized for high-performance import into relational databases.
Main Results:
- mres2x provides a high-throughput solution for Mascot data conversion.
- Generated tabular data allows for complex SQL queries and extensive analysis.
- The program supports extraction of peak lists in DTA format and splitting of Mascot files.
Conclusions:
- Database integration of MS/MS results enables flexible data regrouping.
- Complex analyses can be performed using SQL without rerunning Mascot searches.
- mres2x offers a valuable tool for computational proteomics research.