Assessment and Refinement of Sample Preparation Methods for Deep and Quantitative Plant Proteome Profiling

Proteomics. 2018 Sep;18(17):e1800220. doi: 10.1002/pmic.201800220. Epub 2018 Aug 27.

Abstract

A major challenge in the field of proteomics is obtaining high-quality peptides for comprehensive proteome profiling by LC-MS. Here, evaluation and modification of a range of sample preparation methods using photosynthetically active Arabidopsis leaf tissue are done. It was found that inclusion of filter-aided sample preparation (FASP) based on filter digestion improves all protein extraction methods tested. Ultimately, a detergent-free urea-FASP approach that enables deep and robust quantification of leaf and root proteomes is shown. For example, from 4-day-old leaf tissue, up to 11 690 proteins were profiled from a single sample replicate. This method should be broadly applicable to researchers working with difficult to process plant samples.

Keywords: 2D-LC-MS/MS; Arabidopsis thaliana; mass spectrometry; plant proteomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / growth & development
  • Arabidopsis / metabolism*
  • Arabidopsis Proteins / metabolism*
  • Detergents / chemistry
  • Filtration
  • Plant Leaves / growth & development
  • Plant Leaves / metabolism*
  • Plant Roots / growth & development
  • Plant Roots / metabolism*
  • Proteome / analysis
  • Proteome / metabolism*
  • Specimen Handling / methods*

Substances

  • Arabidopsis Proteins
  • Detergents
  • Proteome