Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12031-6. doi: 10.1073/pnas.1406418111. Epub 2014 Aug 4.


Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a growing class of natural products that are found in all domains of life. These compounds possess vast structural diversity and have a wide range of biological activities, promising a fertile ground for exploring novel natural products. One challenging aspect of RiPP research is the difficulty of structure determination due to their architectural complexity. We here describe a method for automated structural characterization of RiPPs by tandem mass spectrometry. This method is based on the combined analysis of multiple mass spectra and evaluation of a collection of hypothetical structures predicted based on the biosynthetic gene cluster and molecular weight. We show that this method is effective in structural characterization of complex RiPPs, including lanthipeptides, glycopeptides, and azole-containing peptides. Using this method, we have determined the structure of a previously structurally uncharacterized lanthipeptide, prochlorosin 1.2, and investigated the order of the posttranslational modifications in three biosynthetic systems.

Keywords: dehydration; directionality; genome mining; lantibiotics.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Biological Products / chemistry*
  • Biological Products / metabolism
  • Molecular Sequence Data
  • Molecular Structure
  • Peptides / chemistry*
  • Peptides / metabolism
  • Ribosomes / metabolism*
  • Tandem Mass Spectrometry / methods*


  • Biological Products
  • Peptides