Group software

MASH Explorer

The MASH software series is a freely available collection of data analysis tool for both native and denatured top-down proteomics. Beginning with MASH Suite then MASH Suite Pro, NIH support enabled the release of MASH Explorer, a comprehensive and user-friendly tool for denatured top-down proteomics. MASH Explorer can process data from various vendors and incorporates multiple algorithms for deconvolution and database searching. Flexible data reporting options allow easy data interaction through an intuitive graphical user interface.

The latest offering in the MASH series, MASH Native, is an all-in-one software for native top-down proteomics, complex-down analysis, native intact MS, and denatured top-down. The downloadable MASH Native App is a "one-stop-shop", capable of processing data from various vendor-specific and non-specific formats, and incorporating multiple algorithms for deconvolution and database searching. It is developed by an interdisciplinary team consisting of experts in top-down mass spectrometry-based proteomics, computational data science, bioinformatics and biostatistics.

The Ge Lab was awarded NIH R01GM125085-01A1 for MASH Explorer software development.

Please visit the MASH website HERE, supported by the grant. The website features user guides, tutorial videos, example videos, and a user support forum.

https://labs.wisc.edu/gelab/MASH_Explorer/index.php
MASH Explorer USER AGREEMENT

Please cite the following publication if the software is used: Wu, Z.; Roberts, D.S.; Melby, J.A.; Wenger, K.; Wetzel, M.; Gu, Y.; Ramanathan, S.G.; Bayne, E.F.; Liu, X.; Sun, R.; Ong, I.M.; McIlwain, S.J.; Ge, Y. MASH Explorer: A Universal Software Environment for Top-Down Proteomics., J. Proteome Res., 2020, 19 (9), 3867-3876. Article.
The development of MASH Explorer was supported by the National Institutes of Health, grant number R01GM125085. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

The End User Licensing Agreement can be found here.

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MASH Software Publications

  • Wu, Z.; Roberts, D.S.; Melby, J.A.; Wenger, K.; Wetzel, M.; Gu, Y.; Ramanathan, S.G.; Bayne, E.F.; Liu, X.; Sun, R.; Ong, I.M.; McIlwain, S.J.; Ge, Y. MASH Explorer: A Universal Software Environment for Top-Down Proteomics., J. Proteome Res., 2020, 19 (9), 3867-3876. Link

  • S. J. McIlwain, Z. Wu, M. Wetzel, D. Belongia, Y. Jin, K. Wenger, I. Ong, Y. Ge, Enhancing Top-down Proteomics Data Analysis by Combining Deconvolution Results through a Machine Learning Strategy, Journal of the American Society for Mass Spectrometry, 2020, 31, 5, 1104-1113. Link

  • W. Cai, H. Guner, Z. R. Gregorich, A. J. Chen, S. Ayaz-Guner, Y. Peng, S. G. Valeja, X. Liu, Y. Ge. MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics. Molecular & Cellular Proteomics, 2016, 15, 703-714. Link

  • H. Guner, P. L. Close, W. Cai, H. Zhang, Y. Peng, Z. R. Gregorich, Y. Ge. MASH Suite: A User-Friendly and Versatile Software Interface for High-Resolution Mass Spectrometry Data Interpretation and Visualization. Journal of the American Society for Mass Spectrometry, 2014, 25, 464-470. Link