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

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

Author information

1
Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.
2
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48823, USA.

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

PMID:
30035338
PMCID:
PMC6296749
DOI:
10.1002/pmic.201800220
[Indexed for MEDLINE]
Free PMC Article

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