title: Evaluating nonpolar surface area and liquid chromatography/mass spectrometry response: an application for site occupancy measurements for enzyme intermediates in polyketide biosynthesis.
abstract: BACKGROUND
  Site occupancy measurements using liquid chromatography/mass spectrometry (LC/MS) are reported throughout the literature. However, site occupancy quantification suffers from ionization bias between modified and unmodified peptides containing the active site. In this study, we explore the MS signal as a function of nonpolar surface area (NPSA) in order to better understand this bias in electrospray response. The correlation between hydrophobicity and LC/MS response was evaluated and applied to study enzyme intermediates in polyketide synthases.
  
  
  METHODS
  Site occupancy methods were developed to study acyltransferase activity. To further evaluate these methods, several standard peptides containing one cysteine residue were modified with alkylation reagents of increasing hydrophobicity to study the MS signal as a function of NPSA.
  
  
  RESULTS
  A consistent trend in MS response was observed which is dependent on the NPSA of the analyte. An optimal NPSA zone was observed for the peptides studied.
  
  
  CONCLUSIONS
  Nonpolar surface area can be used as metric to determine relative LC/MS response for peptides and evaluate site occupancy measurements.
authors.affiliation: W.M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA; Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: Shan M
authors.initials: SM
authors.lastname: Randall
authors.forename: Irina
authors.initials: I
authors.lastname: Koryakina
authors.forename: Gavin J
authors.initials: GJ
authors.lastname: Williams
authors.forename: David C
authors.initials: DC
authors.lastname: Muddiman
mesh_terms: D000217:Acyltransferases / Q000378:metabolism; D002853:Chromatography, Liquid / Q000379:methods*; D005374:Filtration; D057927:Hydrophobic and Hydrophilic Interactions; D013058:Mass Spectrometry / Q000379:methods*; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D061065:Polyketides / Q000737:chemistry / Q000378:metabolism*
chemical_list: D009842:Oligopeptides; D010446:Peptide Fragments; D061065:Polyketides; D000217:Acyltransferases