Publication details

SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS

Authors

MIKULÁŠEK Kamil KONEČNÁ Hana POTĚŠIL David HOLÁNKOVÁ Renata HAVLIŠ Jan ZDRÁHAL Zbyněk

Year of publication 2021
Type Article in Periodical
Magazine / Source Frontiers in Plant Science
MU Faculty or unit

Central European Institute of Technology

Citation
Web fulltext
Doi http://dx.doi.org/10.3389/fpls.2021.635550
Keywords bottom-up; protein cleanup; Arabidopsis thaliana; sodium dodecyl sulfate removal; single-pot solid-phase-enhanced sample preparation; carboxylated magnetic beads; filter-aided sample preparation; mass spectrometry
Description Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal and protein digestion from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient 2-h SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust the amount of beads, binding and rinsing conditions, or digestion parameters.
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