Progress in Top-Down Proteomics and the Analysis of Proteoforms

Timothy K. Toby, Luca Fornelli, Neil L. Kelleher

Research output: Contribution to journalReview articlepeer-review

397 Scopus citations


From a molecular perspective, enactors of function in biology are intact proteins that can be variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 years, mass spectrometry (MS) has become a powerful method for the analysis of proteomes. Prevailing bottom-up proteomics operates at the level of the peptide, leading to issues with protein inference, connectivity, and incomplete sequence-modification information. Top-down proteomics (TDP), alternatively, applies MS at the proteoform level to analyze intact proteins with diverse sources of intramolecular complexity preserved during analysis. Fortunately, advances in prefractionation workflows, MS instrumentation, and dissociation methods for whole-protein ions have helped TDP emerge as an accessible and potentially disruptive modality with increasingly translational value. In this review, we discuss technical and conceptual advances in TDP, along with the growing power of proteoform-resolved measurements in clinical and translational research.

Original languageEnglish (US)
Pages (from-to)499-519
Number of pages21
JournalAnnual Review of Analytical Chemistry
StatePublished - Jun 12 2016


  • Intact protein analysis
  • Mass spectrometry
  • Proteoforms
  • Top-down proteomics
  • Translational proteomics

ASJC Scopus subject areas

  • Analytical Chemistry


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