Quantitative Proteomics Analysis Protocol

Total protein extracts were prepared as previously described [36 (link)] employing a combination of phenol/acetone/TCA extraction. Digested peptides were measured using a 15 cm C18 Zorbax column (Agilent, Santa Clara, CA, USA), a Dionex Ultimate 3000 RSLC nano-UPLC system (Thermo Fisher, Waltham, MA, USA), a qTOF maXis Impact mass spectrometer (Bruker, Bremen, Germany), or the Orbitrap Fusion Lumos Tribrid Mass Spectrometer (Thermo Fisher) as described previously [37 (link),38 (link)].

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Berka M., Greplová M., Saiz-Fernández I., Novák J., Luklová M., Zelená P., Tomšovský M., Brzobohatý B, & Černý M. (2020). Peptide-Based Identification of Phytophthora Isolates and Phytophthora Detection in Planta. International Journal of Molecular Sciences, 21(24), 9463.

Publication 2020

C18 Zorbax column Dionex Ultimate 3000 RSLC nano-UPLC system Orbitrap Fusion Lumos Tribrid Mass Spectrometer

Acetone Peptides Phenol Protein

Corresponding Organization : Mendel University in Brno

Other organizations : Potato Research Institute, Central European Institute of Technology, Czech Academy of Sciences, Institute of Biophysics

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Variable analysis

independent variables

Combination of phenol/acetone/TCA extraction method used to prepare total protein extracts

dependent variables

Measured digested peptides using a 15 cm C18 Zorbax column, Dionex Ultimate 3000 RSLC nano-UPLC system, qTOF maXis Impact mass spectrometer, or Orbitrap Fusion Lumos Tribrid Mass Spectrometer

control variables

Not explicitly mentioned

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

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