Differential protein analysis of MALDI-TOF mass spectra of bacteria.
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[R] (https://www.r-project.org/). As an alternative, the latest version of [Microsoft R Open] (https://mran.microsoft.com/open/) should be fine.
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[RStudio] (https://www.rstudio.com/) is recommended but optional.
If you have everything installed, you can run identification for a sample spectrum as follows:
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Run [main.R] (main.R) to load the functions.
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Peak alignment. alignment.R outputs peak intensity table compatible with statistical analysis tools, e.g. MetaboAnalyst.
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Differential protein identification. matching.R matches m/z of peaks to protein/peptide sequences from fasta files.
- Yang, Y., Lin, Y., Chen, Z., Gong, T., Yang, P., Girault, H., Liu, B., Qiao, L. Bacterial whole cell typing by mass spectra pattern matching with bootstrapping assessment. Anal Chem 89, 12556–12561 (2017). https://doi.org/10.1021/acs.analchem.7b03820.
- Zhang, D., Yang, Y., Qin, Q., Xu, J., Wang, B., Chen, J., Liu, B., Zhang, W., Qiao, L. MALDI-TOF characterization of protein expression mutation during morphological changes of bacteria under the impact of antibiotics. Anal Chem 91, 2352–2359 (2019). https://doi.org/10.1021/acs.analchem.8b05080.
BacteriaMS-difference is distributed under a BSD license. See the LICENSE file for details.
Please report any problems directly to the github issue tracker. Also, you can send feedback to liang_qiao@fudan.edu.cn.