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

Volumn 25, Issue 3, 2014, Pages 464-470

  Guner, Huseyin ^a   Close, Patrick L ^a   Cai, Wenxuan ^a   Zhang, Han ^a,b   Peng, Ying ^a   Gregorich, Zachery R ^a,b   Ge, Ying ^a,b  

^a UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Bioinformatics; Data processing; Electron capture dissociation; Tandem mass spectrometry; Top down mass spectrometry

Indexed keywords

PROTEINS; PROTEOMICS; SOFTWARE; TANDEM MASS SPECTROMETRY; USER-COMPUTER INTERFACE;

EID: 84894470909     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-013-0789-4     Document Type: Article

References (16)

1. Xian, F.; Hendrickson, C.L.; Marshall, A.G.: High resolution mass spectrometry. Anal. Chem. 84, 708-719 (2012)
2. 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)
3. 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)
4. Siuti, N.; Kelleher, N.L.: Decoding protein modifications using top-down mass spectrometry. Nat. Methods 4, 817-821 (2007)
5. 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)
6. 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)
7. 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)
8. 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)
9. 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)
10. 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)
11. 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)
12. 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)
13. 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)
14. 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)
15. 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)
16. 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)