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

J 2023

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 et. al.

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

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

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

Abstract

V originále

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

Citovat

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.

@article{2364078,
   author = {Martinková, Petra and Konečná, Hana and Gintar, Petr and Kryštofová, Karolína and Potěšil, David and Trtílek, Martin and Zdráhal, Zbyněk},
   article_number = {24},
   doi = {http://dx.doi.org/10.3390/ijms242417347},
   keywords = {peptide clean-up; magnetic beads; SP2; ethyl acetate extraction; sodium dodecyl sulfate; detergent; polyethylene glycol; Arabidopsis thaliana; LC-MS/MS},
   language = {eng},
   issn = {1661-6596},
   journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
   title = {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},
   url = {https://www.mdpi.com/1422-0067/24/24/17347},
   volume = {24},
   year = {2023}
}

TY  - JOUR
ID  - 2364078
AU  - Martinková, Petra - Konečná, Hana - Gintar, Petr - Kryštofová, Karolína - Potěšil, David - Trtílek, Martin - Zdráhal, Zbyněk
PY  - 2023
TI  - 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
JF  - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
VL  - 24
IS  - 24
SP  - "17347"
EP  - "17347"
PB  - MDPI
SN  - 16616596
KW  - peptide clean-up
KW  - magnetic beads
KW  - SP2
KW  - ethyl acetate extraction
KW  - sodium dodecyl sulfate
KW  - detergent
KW  - polyethylene glycol
KW  - Arabidopsis thaliana
KW  - LC-MS/MS
UR  - https://www.mdpi.com/1422-0067/24/24/17347
N2  - 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.
ER  -

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. \textit{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.

Detailed Information on Publication Record