Bioinformatics analysis of top-down mass spectrometry data with proSight lite

Caroline J. Dehart, Ryan T. Fellers, Luca Fornelli, Neil L. Kelleher, Paul M. Thomas*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

23 Scopus citations


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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages14
StatePublished - 2017

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Bioinformatics
  • Intact protein
  • Mass spectrometry
  • ProSight lite
  • Proteomics
  • Top-down

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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