MASH Explorer

MASH Native: A Universal Software for Native Top-Down Proteomics

MASH Native is a comprehensive and user-friendly software environment for native and denatured top-down proteomics, which includes a downloadable software package, MASH Native App, that acts as a ‘one-stop shop’ for top-down proteomics. Thus, providing users with a free, easy-to-use, universal software platform, MASH eliminates a significant barrier to new native top-down proteomics users and streamlining data processing for expert users. The software has the capability to process data from various vendor formats with ProteoWizard and incorporate multiple algorithms for deconvolution, database searching, spectral averaging, and characterization of native complexes and proteoforms.

MASH Native has expanded from our previous developments of MASH Suite, MASH Suite Pro, and MASH Explorer to incorporate the UniDec deconvolution algorithm to process both isotopically resolved and unresolved MS1 data. MASH can process both native top-down MS/MS data which directly dissociates the proteins and protein complexes in the gas phase, and “complex-down” data analyzing MS1 (intact mass measurement of protein complexes), MS2 (dissociation into subunits), and MS3 (fragmentation of proteoforms). MASH Native provides the first tool capable of deconvolution and database searching for native top-down and complex-down data in discovery mode, in addition to analysis of native top-down and complex-down data in the targeted mode. Features such as internal fragment searching have enabled greater sequence coverage of native proteins by MS2 and MS3 with enhanced confidence in localization of PTMs.

It is developed by an interdisciplinary team from the Ying Ge Lab and collaborators, consisting of experts in top-down mass spectrometry-based proteomics, computational data science, and bioinformatics/biostatistics. The Ge lab would like to acknowledge funding from NIH R01 grant (GM125085) to allow the continuous development of MASH Native.

Installation Requirements and MASH Native Setup Guide

Getting Started with MASH Native, a Quick Tutorial

User Resources

Contact the MASH Team

End User Licensing Agreement

MASH App Privacy Notice

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The National Institutes of Health reserves a royalty-free, non-exclusive and irrevocable license for the federal government to reproduce, publish or otherwise use the work for federal purposes, and to authorize others to do so. The MASH software project is supported by NIH GM125085.

Legacy MASH Software:

Access and download MASH Suite, MASH Suite Pro, and MASH Explorer the foundation of MASH Native.

Key references:

MASH Software Series

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

UniDec Series

M. T. Marty , A. J. Baldwin , E. G. Marklund , G. K. A. Hochberg , J. L. P. Benesch , and C. V. Robinson."Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles"Analytical Chemistry, 2015, DOI: 10.1021/acs.analchem.5b00140.

D. J. Reid, J. M. Diesing, M. A. Miller, S. M. Perry, J. A. Wales, W. R. Montfort, M. T. Marty." MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra" Journal of the American Society for Mass Spectrometry, 2019, DOI: https://doi.org/10.1007/s13361-018-1951-9

TopPIC

Q. Kou, L. Xun, and X. Liu. TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization. Bioinformatics, 2016, 32 , 3495-3497.
https://www.ncbi.nlm.nih.gov/pubmed/27423895

MS-Align

X. Liu, Y. Sirotkin, Y. Shen, G. Anderson, Y. S. Tsai, Y. S. Ting, D. R. Goodlett, R. D. Smith, V. Bafna, and P. A. Pevzner. Protein Identification Using Top-Down Spectra. Molecular & Cellular Proteomics, 2012, 11: 6
http://www.mcponline.org/content/11/6/M111.008524

MSDeconv

X. Liu, Y. Inbar, P. C. Dorrestein, C. Wynne, N. Edwards, P.Souda, J. P. Whitelegge, V. Bafna, and P. A. Pevzner. Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins. Molecular & Cellular Proteomics , 2010, 9, 12: 2772-2782.
http://www.mcponline.org/content/early/2010/09/20/mcp.M110.002766

FLASHDeconv

K. Jeong, J. Kim, M. Gaikwad, S. N. Hidayah, L. Heikaus, H. Schlüter, and O. Kohlbacher, “FLASHDeconv: Ultrafast, high-quality feature deconvolution for top-down proteomics,” Cell Systems, vol. 10, iss. 2, p. 213–218, 2020.
https://www.cell.com/cell-systems/pdfExtended/S2405-4712(20)30030-2

ProteoWizard

M.C. Chambers, B. MacLean, R. Burke, D. Amode, D.L. Ruderman, S. Neumann, L. Gatto, B. Fischer, B.Pratt, J. Egertson, K. Hoff, D. Kessner, N. Tasman, N. Shulman, B. Frewen, T.A. Baker, M.-Y. Brusniak, C. Paulse, D. Creasy, L. Flashner,K. Kani, C. Moulding, S. L.Seymour, L. M. Nuwaysir, B. Lefebvre, F. Kuhlmann, J. Roark, P. Rainer, S. Detlev, T. Hemenway, A. Huhmer, J. Langridge, B. Connolly, T. Chadick, K. Holly, J. Eckels, E. W. Deutsch, R. L. Moritz, J. E. Katz, D. B. Agus, M. MacCoss, D. L. Tabb, & P. Mallick. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology, 2012, 30, 918-920.
https://www.nature.com/articles/nbt.2377

THRASH

D. M. Horn, R. A. Zubarev, and F. W. McLafferty. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules, Journal of the American Society for Mass Spectrometry, 2000, 11: 4, 320-332.
https://www.sciencedirect.com/science/article/pii/S1044030505009840

Informed Proteomics

J. Park, P. D. Piehowski, C. Wilkins, M. Zhou, J. Mendoza, G. M. Fujimoto, B. C. Gibbons, J. B. Shaw, Y. Shen, A. K. Shukla, R. J. Moore, T. Liu, V. A. Petyuk, N. Tolic, L. Pasa-Tolic, R. D. Smith, S. H. Payne, and S. Kim. Informed-Proteomics: Open Source Software Package for Top-down Proteomics. Nature Methods, 2017, 14: 9. 909-914
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578875/

RawFileReader

CompassXtract

DeconEngine

N. Jaitly, A. Mayampurath, K. Littlefield, J. N. Adkins, G. A. Anderson, and R. D. Smith. Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics, 2009, 10: 87.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666663/

MSFileReader

MSFileReader file reading tool. Copyright © 2009 - 2014 by Thermo Fisher Scientific, Inc. All rights reserved.
https://thermo.flexnetoperations.com/control/thmo/login?nextURL=/control/thmo/download?element=6306677

pParseTD

Z.-F. Yuan, C. Liu, H.-P. Wang, R.-X. Sun, Y. Fu, J.-F. Zhang, L.-H. Wang, H. Chi, Y. Li, L.-Y. Xiu, W.-P. Wang, S.-M. He. pParse: a method for accurate determination of monoisotopic peaks in high-resolution mass spectra. Proteomics , 2012, 12: 2, 226–235
https://onlinelibrary.wiley.com/doi/abs/10.1002/pmic.201100081

pTOP

pTop 1.0: a High-accuracy and High-efficiency Search Engine for Intact Protein Identification. R.-X. Sun, L. Luo, L. Wu, R.-M. Wang, W.-F. Zeng, H. Chi, C. Liu, and S.-M. He. Analytical Chemistry, 2016, 88, 3082-3090.
https://www.ncbi.nlm.nih.gov/pubmed/26844380