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

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.

SUBMITTER: Song G

PROVIDER: S-EPMC6296749 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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

Song Gaoyuan G Hsu Polly Yingshan PY Walley Justin W JW

Proteomics 20180827 17

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 quantificat ...[more]

PMID: 30035338

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