Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite

Part of the Methods in Molecular Biology book series (MIMB, volume 1558)


Traditional bottom-up mass spectrometry-based proteomics relies on the use of an enzyme, often trypsin, to generate small peptides (typically < 25 amino acids long). In top-down proteomics, proteins remain intact and are directly measured within the mass spectrometer. This technique, while inherently simpler than bottom-up proteomics, generates data which must be processed and analyzed using software tools “purpose-built” for the job. In this chapter, we will show the analysis of intact protein spectra through deconvolution, deisotoping, and searching with ProSight Lite, a free, vendor-agnostic tool for the analysis of top-down mass spectrometry data. We will illustrate with two examples of intact protein fragmentation spectra and discuss the iterative use of the software to characterize proteoforms and discover the sites of post-translational modifications.

Key words

Top-down Mass spectrometry Proteomics ProSight Lite Intact protein Bioinformatics 



The authors are grateful to members of the Kelleher Research Group/Proteomics Center of Excellence for helpful discussions, particularly Joseph Greer, Richard LeDuc, and Bryan Early. This work was supported by Award No. P41GM108569 from the National Institute of General Medical Sciences The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.


  1. 1.
    Erickson BK, Jedrychowski MP, McAlister GC, Everley RA, Kunz R, Gygi SP (2015) Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer. Anal Chem 87(2):1241–1249. doi: 10.1021/ac503934f CrossRefPubMedGoogle Scholar
  2. 2.
    Beck S, Michalski A, Raether O, Lubeck M, Kaspar S, Goedecke N, Baessmann C, Hornburg D, Meier F, Paron I, Kulak NA, Cox J, Mann M (2015) The impact II, a very high-resolution quadrupole time-of-flight instrument (QTOF) for deep shotgun proteomics. Mol Cell Proteomics 14(7):2014–2029. doi: 10.1074/mcp.M114.047407 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Kelleher NL (2004) Top-down proteomics. Anal Chem 76(11):197A–203ACrossRefPubMedGoogle Scholar
  4. 4.
    LM S, NL K, Consortium for Top Down P (2013) Proteoform: a single term describing protein complexity. Nat Methods 10(3):186–187. doi: 10.1038/nmeth.2369 CrossRefGoogle Scholar
  5. 5.
    Zheng Y, Fornelli L, Compton PD, Sharma S, Canterbury J, Mullen C, Zabrouskov V, Fellers RT, Thomas PM, Licht JD, Senko MW, Kelleher NL (2015) Unabridged analysis of human histone H3 by differential top-down mass spectrometry reveals hypermethylated proteoforms from MMSET/NSD2 overexpression. Mol Cell Proteomics. doi: 10.1074/mcp.M115.053819 Google Scholar
  6. 6.
    Dang X, Scotcher J, Wu S, Chu RK, Tolic N, Ntai I, Thomas PM, Fellers RT, Early BP, Zheng Y, Durbin KR, Leduc RD, Wolff JJ, Thompson CJ, Pan J, Han J, Shaw JB, Salisbury JP, Easterling M, Borchers CH, Brodbelt JS, Agar JN, Pasa-Tolic L, Kelleher NL, Young NL (2014) The first pilot project of the consortium for top-down proteomics: a status report. Proteomics 14(10):1130–1140. doi: 10.1002/pmic.201300438 CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Tian Z, Tolic N, Zhao R, Moore RJ, Hengel SM, Robinson EW, Stenoien DL, Wu S, Smith RD, Pasa-Tolic L (2012) Enhanced top-down characterization of histone post-translational modifications. Genome Biol 13(10):R86. doi: 10.1186/gb-2012-13-10-r86 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Barnidge DR, Dasari S, Botz CM, Murray DH, Snyder MR, Katzmann JA, Dispenzieri A, Murray DL (2014) Using mass spectrometry to monitor monoclonal immunoglobulins in patients with a monoclonal gammopathy. J Proteome Res 13(3):1419–1427. doi: 10.1021/pr400985k CrossRefPubMedGoogle Scholar
  9. 9.
    Fornelli L, Damoc E, Thomas PM, Kelleher NL, Aizikov K, Denisov E, Makarov A, Tsybin YO (2012) Analysis of intact monoclonal antibody IgG1 by electron transfer dissociation Orbitrap FTMS. Mol Cell Proteomics 11(12):1758–1767. doi: 10.1074/mcp.M112.019620 CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Zhang H, Cui W, Gross ML (2014) Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies. FEBS Lett 588(2):308–317. doi: 10.1016/j.febslet.2013.11.027 CrossRefPubMedGoogle Scholar
  11. 11.
    Ansong C, Wu S, Meng D, Liu X, Brewer HM, Deatherage Kaiser BL, Nakayasu ES, Cort JR, Pevzner P, Smith RD, Heffron F, Adkins JN, Pasa-Tolic L (2013) Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions. Proc Natl Acad Sci U S A 110(25):10153–10158. doi: 10.1073/pnas.1221210110 CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Cheon DH, Nam EJ, Park KH, Woo SJ, Lee HJ, Kim HC, Yang EG, Lee C, Lee JE (2015) Comprehensive analysis of low-molecular-weight human plasma proteome using top-down mass spectrometry. J Proteome Res. doi: 10.1021/acs.jproteome.5b00773 PubMedGoogle Scholar
  13. 13.
    Tran JC, Zamdborg L, Ahlf DR, Lee JE, Catherman AD, Durbin KR, Tipton JD, Vellaichamy A, Kellie JF, Li M, Wu C, Sweet SM, Early BP, Siuti N, LeDuc RD, Compton PD, Thomas PM, Kelleher NL (2011) Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 480(7376):254–258. doi: 10.1038/nature10575 CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Liu X, Hengel S, Wu S, Tolic N, Pasa-Tolic L, Pevzner PA (2013) Identification of ultramodified proteins using top-down tandem mass spectra. J Proteome Res 12(12):5830–5838. doi: 10.1021/pr400849y CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Zamdborg L, LeDuc RD, Glowacz KJ, Kim YB, Viswanathan V, Spaulding IT, Early BP, Bluhm EJ, Babai S, Kelleher NL (2007) ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry. Nucleic Acids Res 35(Web Server issue):W701–W706. doi: 10.1093/nar/gkm371 CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Cannon JR, Holden DD, Brodbelt JS (2014) Hybridizing ultraviolet photodissociation with electron transfer dissociation for intact protein characterization. Anal Chem 86(21):10970–10977. doi: 10.1021/ac5036082 CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Fellers RT, Greer JB, Early BP, Yu X, LeDuc RD, Kelleher NL, Thomas PM (2015) ProSight lite: graphical software to analyze top-down mass spectrometry data. Proteomics 15(7):1235–1238. doi: 10.1002/pmic.201570050 CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS (2005) The universal protein resource (UniProt). Nucleic Acids Res 33(Database issue):D154–D159. doi: 10.1093/nar/gki070 CrossRefPubMedGoogle Scholar
  19. 19.
    Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA (2010) Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Mol Cell Proteomics: MCP 9(12):2772–2782. doi: 10.1074/mcp.M110.002766 CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Carvalho PC, Xu T, Han X, Cociorva D, Barbosa VC, Yates JR 3rd (2009) YADA: a tool for taking the most out of high-resolution spectra. Bioinformatics 25(20):2734–2736. doi: 10.1093/bioinformatics/btp489 CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Kessner D, Chambers M, Burke R, Agus D, Mallick P (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24(21):2534–2536. doi: 10.1093/bioinformatics/btn323 CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Roepstorff P, Fohlman J (1984) Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11(11):601. doi: 10.1002/bms.1200111109 CrossRefPubMedGoogle Scholar
  23. 23.
    Meng F, Cargile BJ, Miller LM, Forbes AJ, Johnson JR, Kelleher NL (2001) Informatics and multiplexing of intact protein identification in bacteria and the archaea. Nat Biotechnol 19(10):952–957. doi: 10.1038/nbt1001-952 CrossRefPubMedGoogle Scholar

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© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Departments of Chemistry, Molecular Biosciences, the Proteomics Center of Excellence and the Robert H. Lurie Comprehensive Cancer Center at the Feinberg School of MedicineNorthwestern UniversityEvanstonUSA

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