title: Achieving efficient digestion faster with Flash Digest: potential alternative to multi-step detergent assisted in-solution digestion in quantitative proteomics experiments.
abstract: BACKGROUND
  In quantitative analysis of protein biomarkers and therapeutic proteins by liquid chromatography/mass spectrometry (LC/MS), it is a preferred and well-established approach to digest with proteolytic enzymes to produce smaller peptide fragments which are more suitable for LC/MS analysis than the intact protein. In-solution digestion is one widely used method for protein digestion. Proteolytically resistant proteins often require digestion times that extend beyond normal working hours and prohibit same day analysis. We evaluated the performance of an immobilized enzyme reactor (IMER) to determine if this technology could reduce method development time, digestion time and increase throughput.
  
  
  METHODS
  We digested human plasma samples using a commercially available IMER, Flash Digest, and compared it to an in-solution digestion method for analysis of three different apolipoprotein biomarkers APOE, APOC2, and APOC3. The plasma digests were analyzed via LC/MS using electrospray ionization (ESI) and multiple reaction monitoring (MRM). Value assigned calibrators were selected over a relevant physiological concentration range for each protein of interest. Quality control samples (QCs) and 'unknown' human plasma samples were analyzed with both methods.
  
  
  RESULTS
  Flash Digest significantly reduced digestion time for APOC3, the most proteolytically resistant of the three proteins, to 30 min compared with overnight used with in-solution digestion. The Flash Digest achieved comparable digestion efficiency with minimal method development and reduced sample preparation time. Both methods showed linearity over a physiologically relevant concentration range. Precision was evaluated and a percentage coefficient of variance (% CV) less than 8% was obtained during intra-day reproducibility evaluation for all three apolipoproteins with Flash Digest. Concentrations observed for QCs and unknown samples using Flash Digest were comparable to the in-solution method.
  
  
  CONCLUSIONS
  An IMER such as Flash Digest may be a potential alternative to in-solution digestion to accelerate digestion of proteolytically resistant proteins in a quantitative proteomics experiments, reduce method development time and increase throughput. Copyright © 2016 John Wiley & Sons, Ltd.
authors: Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, NJ, USA.
authors: Vinit
authors: V
authors: Shah
authors: Translational Molecular Biomarkers, Merck Research Laboratories, Kenilworth, NJ, USA.
authors: Michael E
authors: ME
authors: Lassman
authors: Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, NJ, USA.
authors: Ying
authors: Y
authors: Chen
authors: Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, NJ, USA.
authors: Haihong
authors: H
authors: Zhou
authors: Translational Molecular Biomarkers, Merck Research Laboratories, Kenilworth, NJ, USA.
authors: Omar F
authors: OF
authors: Laterza
mesh_terms: D015415:Biomarkers; D002853:Chromatography, Liquid / Q000379:methods*; D003902:Detergents; D004800:Enzymes, Immobilized / Q000378:metabolism; D056945:Hep G2 Cells; D006801:Humans; D016014:Linear Models; D013058:Mass Spectrometry / Q000379:methods*; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D059748:Proteolysis; D020543:Proteome / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D014357:Trypsin / Q000378:metabolism
chemical_list: D015415:Biomarkers; D003902:Detergents; D004800:Enzymes, Immobilized; D010446:Peptide Fragments; D020543:Proteome; D014357:Trypsin