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

Kamil Mikulášek; Hana Konečná; David Potěšil; Renata Holánková; Jan Havliš; Zbyněk Zdráhal

doi:10.3389/fpls.2021.635550

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

Front Plant Sci. 2021 Mar 10:12:635550. doi: 10.3389/fpls.2021.635550. eCollection 2021.

Authors

Kamil Mikulášek^{1

2}, Hana Konečná^{1

2}, David Potěšil¹, Renata Holánková¹, Jan Havliš², Zbyněk Zdráhal^{1

2}

Affiliations

¹ Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia.
² National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia.

Abstract

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.

Keywords: Arabidopsis thaliana; bottom-up; carboxylated magnetic beads; filter-aided sample preparation; mass spectrometry; protein cleanup; single-pot solid-phase-enhanced sample preparation; sodium dodecyl sulfate removal.