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.

Základní údaje

Originální název

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

Autoři

MARTINKOVÁ, Petra (203 Česká republika, domácí), Hana KONEČNÁ (203 Česká republika, domácí), Petr GINTAR (203 Česká republika, domácí), Karolína KRYŠTOFOVÁ (203 Česká republika, domácí), David POTĚŠIL (203 Česká republika, domácí), Martin TRTÍLEK (203 Česká republika) a Zbyněk ZDRÁHAL (203 Česká republika, garant, domácí)

Vydání

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, MDPI, 2023, 1661-6596

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

fulltext

Impakt faktor

Impact factor: 5.600 v roce 2022

Kód RIV

RIV/00216224:14740/23:00133126

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.3390/ijms242417347

UT WoS

001132258900001

Klíčová slova anglicky

peptide clean-up; magnetic beads; SP2; ethyl acetate extraction; sodium dodecyl sulfate; detergent; polyethylene glycol; Arabidopsis thaliana; LC-MS/MS

Štítky

CF PROT, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 2. 11. 2024 20:14, Ing. Martina Blahová

Anotace

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.

Návaznosti

EF16_026/0008446, projekt VaV

Název: Integrace signálu a epigenetické reprogramování pro produktivitu rostlin

EF18_072/0015659, projekt VaV

Název: e-INFRA CZ: Modernizace

LM2023042, projekt VaV

Název: Česká infrastruktura pro integrativní strukturní biologii

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CIISB - Česká infrastruktura pro integrativní strukturní biologii

90254, velká výzkumná infrastruktura

Název: e-INFRA CZ II

Citovat

MARTINKOVÁ, Petra, Hana KONEČNÁ, Petr GINTAR, Karolína KRYŠTOFOVÁ, David POTĚŠIL, Martin TRTÍLEK a 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, roč. 24, č. 24, s. "17347", 21 s. ISSN 1661-6596. Dostupné z: 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 a 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, roč.~24, č.~24, s.~''17347'', 21 s. ISSN~1661-6596. Dostupné z: https://dx.doi.org/10.3390/ijms242417347.

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