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mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data
Martin Strohalm1, Daniel Kavan, Petr Novák
1Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic. strohalm@biomed.cas.cz
Analytical Chemistry
|May 15, 2010
Summary
The new mMass software offers precise analysis of mass spectrometry (MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) data. This cross-platform tool enhances spectral examination and data validation for mass spectrometrists.
Area of Science:
- Analytical Chemistry
- Biochemistry
- Computational Biology
Background:
- Automated analysis tools for mass spectrometry (MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are improving.
- Mass spectrometrists often manually examine individual spectra post-experiment.
- Existing software is frequently instrument-dependent and vendor-provided.
Purpose of the Study:
- To introduce a new generation of mMass, a cross-platform software for precise analysis of individual mass spectra.
- To provide a comprehensive environment for various spectral processing tasks.
- To offer improved functionalities for in silico digestion, fragmentation, and compound identification.
Main Methods:
- Development of a cross-platform software environment (mMass).
- Implementation of data processing tasks: import, smoothing, baseline correction, peak picking, deisotoping, charge determination, recalibration.
- Integration of isotopic pattern modeling, in silico digestion/fragmentation, and interfaces for ProFound and Mascot.
- Incorporation of the LIPID MAPS lipid database and a custom compound library search tool.
- Development of a stand-alone Python library for data processing and interpretation.
Main Results:
- mMass provides a wide range of processing tasks for MS and LC-MS/MS data.
- Redesigned and improved in silico digestion and fragmentation functions.
- New interfaces for ProFound and Mascot, plus a tool for isotopic pattern modeling.
- Rapid lipid identification using the LIPID MAPS database and a compound search tool.
- A foundational Python library is available for developers.
Conclusions:
- The new mMass version offers a powerful, cross-platform solution for precise mass spectral analysis.
- It enhances data validation and compound identification capabilities, including lipids.
- The underlying Python library supports further development in mass spectrometry data analysis.
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