Abstract
The rapid advancements in mass spectrometry (MS) instrumentation, particularly in Fourier transform (FT) MS, have made the acquisition of high-resolution and high-accuracy mass measurements routine. However, the software tools for the interpretation of high-resolution MS data are underdeveloped. Although several algorithms for the automatic processing of high-resolution MS data are available, there is still an urgent need for a user-friendly interface with functions that allow users to visualize and validate the computational output. Therefore, we have developed MASH Suite, a user-friendly and versatile software interface for processing high-resolution MS data. MASH Suite contains a wide range of features that allow users to easily navigate through data analysis, visualize complex high-resolution MS data, and manually validate automatically processed results. Furthermore, it provides easy, fast, and reliable interpretation of top-down, middle-down, and bottom-up MS data. MASH Suite is convenient, easily operated, and freely available. It can greatly facilitate the comprehensive interpretation and validation of high-resolution MS data with high accuracy and reliability.
ᅠ
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Xian, F., Hendrickson, C.L., Marshall, A.G.: High resolution mass spectrometry. Anal. Chem. 84, 708–719 (2012)
Hoopmann, M.R., Finney, G.L., MacCoss, M.J.: High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Anal. Chem. 79, 5620–5632 (2007)
Ge, Y., Rybakova, I.N., Xu, Q., Moss, R.L.: Top-down high-resolution mass spectrometry of cardiac myosin binding protein c revealed that truncation alters protein phosphorylation state. Proc. Natl. Acad. Sci. U.S.A. 106, 12658–12663 (2009)
Siuti, N., Kelleher, N.L.: Decoding protein modifications using top-down mass spectrometry. Nat. Methods 4, 817–821 (2007)
Horn, D.M., Zubarev, R.A., McLafferty, F.W.: Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom. 11, 320–332 (2000)
Jaitly, N., Mayampurath, A., Littlefield, K., Adkins, J.N., Anderson, G.A., Smith, R.D.: Decon2LS: an open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics 10, 87 (2009)
Park, K., Yoon, J.Y., Lee, S., Paek, E., Park, H., Jung, H.J., Lee, S.W.: Isotopic peak intensity ratio based algorithm for determination of isotopic clusters and monoisotopic masses of polypeptides from high-resolution mass spectrometric data. Anal. Chem. 80, 7294–7303 (2008)
Mayampurath, A.M., Jaitly, N., Purvine, S.O., Monroe, M.E., Auberry, K.J., Adkins, J.N., Smith, R.D.: DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics 24, 1021–1023 (2008)
Liu, X.W., Inbar, Y., Dorrestein, P.C., Wynne, C., Edwards, N., Souda, P., Whitelegge, J.P., Bafna, V., Pevzner, P.A.: Deconvolution and database search of complex tandem mass spectra of intact proteins. Mol. Cell. Proteom. 9, 2772–2782 (2010)
Senko, M.W., Beu, S.C., McLafferty, F.W.: Automated assignment of charge states from resolved isotopic peaks for multiply-charged ions. J. Am. Soc. Mass Spectrom. 6, 52–56 (1995)
Zhang, Z.Q., Marshall, A.G.: A universal algorithm for fast and automated charge state deconvolution of electrospray mass-to-charge ratio spectra. J. Am. Soc. Mass Spectrom. 9, 225–233 (1998)
Senko, M.W., Beu, S.C., McLafferty, F.W.: Automated assignment of charge states from resolved isotopic peaks for multiply charged ions. J. Am. Soc. Mass Spectrom. 6, 52–56 (1995)
Pesavento, J.J., Mizzen, C.A., Kelleher, N.L.: Quantitative analysis of modified proteins and their positional isomers by tandem mass spectrometry: human histone H4. Anal. Chem. 78, 4271–4280 (2006)
Zhang, J., Guy, M.J., Norman, H.S., Chen, Y.-C., Xu, Q., Dong, X., Guner, H., Wang, S., Kohmoto, T., Young, K.H., Moss, R.L., Ge, Y.: Top-down quantitative proteomics identified phosphorylation of cardiac troponin I as a candidate biomarker for chronic heart failure. J. Proteome Res. 10, 4054–4065 (2011)
Dong, X., Sumandea, C.A., Chen, Y.-C., Garcia-Cazarin, M.L., Zhang, J., Balke, C.W., Sumandea, M.P., Ge, Y.: Augmented phosphorylation of cardiac troponin I in hypertensive heart failure. J. Biol. Chem. 287, 848–857 (2012)
Peng, Y., Chen, X., Zhang, H., Xu, Q., Hacker, T.A., Ge, Y.: Top-down targeted proteomics for deep sequencing of tropomyosin isoforms. J. Proteome Res. 12, 187–198 (2013)
Acknowledgments
The authors thank Yi-chen Chen, Serife Guner, Jiang Zhang, and Matthew Lawrence for helpful discussions, and Santosh Valeja for critical reading of this manuscript. The authors are also grateful to David Horn for his kind assistance at the early stage. Financial support was kindly provided by the Wisconsin Partnership Fund for a Healthy Future, American Heart Association Scientist Development Grant 0735443Z, and NIH R01HL096971 and R01HL109810 (to Y.G.).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Guner, H., Close, P.L., Cai, W. et al. MASH Suite: A User-Friendly and Versatile Software Interface for High-Resolution Mass Spectrometry Data Interpretation and Visualization. J. Am. Soc. Mass Spectrom. 25, 464–470 (2014). https://doi.org/10.1007/s13361-013-0789-4
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13361-013-0789-4