Benchmarking of Two Peptide Clean-Up Protocols: SP2 and Ethyl Acetate Extraction for Sodium Dodecyl Sulfate or Polyethylene Glycol Removal from Plant Samples before LC-MS/MS

MARTINKOVÁ, Petra, Hana KONEČNÁ, Petr GINTAR, Karolína KRYŠTOFOVÁ, David POTĚŠIL, Martin TRTÍLEK and Zbyněk ZDRÁHAL. Benchmarking of Two Peptide Clean-Up Protocols: SP2 and Ethyl Acetate Extraction for Sodium Dodecyl Sulfate or Polyethylene Glycol Removal from Plant Samples before LC-MS/MS. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. MDPI, 2023, vol. 24, No 24, p. "17347", 21 pp. ISSN 1661-6596. Available from: https://dx.doi.org/10.3390/ijms242417347.

Basic information

• Original name: Benchmarking of Two Peptide Clean-Up Protocols: SP2 and Ethyl Acetate Extraction for Sodium Dodecyl Sulfate or Polyethylene Glycol Removal from Plant Samples before LC-MS/MS
• Authors: MARTINKOVÁ, Petra (203 Czech Republic, belonging to the institution), Hana KONEČNÁ (203 Czech Republic, belonging to the institution), Petr GINTAR (203 Czech Republic, belonging to the institution), Karolína KRYŠTOFOVÁ (203 Czech Republic, belonging to the institution), David POTĚŠIL (203 Czech Republic, belonging to the institution), Martin TRTÍLEK (203 Czech Republic) and Zbyněk ZDRÁHAL (203 Czech Republic, guarantor, belonging to the institution).
• Edition: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, MDPI, 2023, 1661-6596.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10608 Biochemistry and molecular biology
• Country of publisher: Switzerland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: fulltext
• Impact factor: Impact factor: 5.600 in 2022
• RIV identification code: RIV/00216224:14740/23:00133126
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.3390/ijms242417347
• UT WoS: 001132258900001
• Keywords in English: peptide clean-up; magnetic beads; SP2; ethyl acetate extraction; sodium dodecyl sulfate; detergent; polyethylene glycol; Arabidopsis thaliana; LC-MS/MS
• Tags: CF PROT, rivok
• Tags: International impact, Reviewed

Abstract

The success of bottom-up proteomic analysis frequently depends on the efficient removal of contaminants from protein or peptide samples before LC-MS/MS. For a peptide clean-up workflow, single-pot solid-phase-enhanced peptide sample preparation on carboxylate-modified paramagnetic beads (termed SP2) was evaluated for sodium dodecyl sulfate or polyethylene glycol removal from Arabidopsis thaliana tryptic peptides. The robust and efficient 40-min SP2 protocol, tested for 10-ng, 250-ng, and 10-µg peptide samples, was proposed and benchmarked thoroughly against the ethyl acetate extraction protocol. The SP2 protocol on carboxylated magnetic beads proved to be the most robust approach, even for the simultaneous removal of massive sodium dodecyl sulfate (SDS) and polyethylene glycol (PEG) contaminations from AT peptide samples in respect of the LC-MS/MS data outperforming ethyl acetate extraction.

Links

• EF16_026/0008446, research and development project: Name: Integrace signálu a epigenetické reprogramování pro produktivitu rostlin
• EF18_072/0015659, research and development project: Name: e-INFRA CZ: Modernizace
• LM2023042, research and development project: Name: Česká infrastruktura pro integrativní strukturní biologii

Investor: Ministry of Education, Youth and Sports of the CR, CIISB - Czech Infrastructure for Integrative Structural Biology

• 90242, large research infrastructures: Name: CIISB III
• 90254, large research infrastructures: Name: e-INFRA CZ II