Jun 09, 2026

Chemical profiling for fungal culture extract

DOI
https://dx.doi.org/10.17504/protocols.io.rm7vzwnj8vx1/v1
  • Clémence ROHÉE1,
  • Alice M.S. Rodrigues1,
  • Yoan FERANDIN1,
  • Emeline HOUEL1,
  • Didier STIEN1,
  • Didier Stien2
  • 1Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Observatoire Océanologique, 66650 Banyuls‑sur‑mer, France;
  • 2CNRS
  • EUREMAP PROTOCOLS COMMUNITY
  • EUREMAP_SU_LBBM
Clémence ROHÉE
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DOI: https://dx.doi.org/10.17504/protocols.io.rm7vzwnj8vx1/v1
Protocol Citation: Clémence ROHÉE, Alice M.S. Rodrigues, Yoan FERANDIN, Emeline HOUEL, Didier STIEN, Didier Stien 2026. Chemical profiling for fungal culture extract. protocols.io https://dx.doi.org/10.17504/protocols.io.rm7vzwnj8vx1/v1
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 08, 2026
Last Modified: June 09, 2026
Protocol  Integer ID: 318698
Keywords: chemical profiling for fungal culture extract chemical analysis, fungal culture extract chemical analysis, fungal culture extract, chemical profiling
Funders Acknowledgements:
EUROPEAN UNION
Grant ID: INFRA-2023-DEV-01-04
Abstract
Chemical analysis of fungal culture extracts for metabolomic studies
Materials
LC-MS-grade Solvents
Chromatography system: UHPLC Ultimate 3000™ (Thermo Scientific)
Mass spectrometer: Orbitrap FT Q-Exactive Focus™ (Thermo Scientific)
Data visualization software: FreeStyle® 1.5
Safety warnings
Use nitrile gloves, safety goggles and lab coat.
Before start
Dry extract are dissolved to a concentration of 1 mg/mL in methanol LCMS-grade. Injection volume is 2 μL.
Sample Preparation
Dry extract are dissolved to a concentration of 1 mg/mL in methanol LCMS-grade. Injection volume is 2 μL.
Chromatographic Conditions
Column: Phenomenex® Kinetex C8 2,6μm 150x2.1mm (Phenomenex)
Column temperature: 40 °C
Flow rate: 0.5 mL/min
Solvents:
A = Water + 0.1% formic acid
B = Acetonitrile + 0.1% formic acid
Gradient:
Mass Spectrometry Conditions
Acquisition mode: Full MS with data-dependent MS/MS acquisition (dd-MS2, Discovery mode)
Ionization mode: Electrospray (ESI+)
Mass range (m/z): 133.4 – 2000 Da
Detection mode: Centroid
Full MS settings:
Resolution: 70,000
AGC target: 3 × 10^6
Internal calibrant: m/z 144.98215 (Cu(CH3CN)2+)
dd-MS2 settings:
Resolution: 17,500
AGC target: 1 × 10^5
Isolation window: 0.4 Da
Normalized collision energies (NCE): 15 / 30 / 40%
Dynamic exclusion: 6 s
ESI source parameters:
Spray voltage: 3 kV
Sheath gas flow rate: 75 (arbitrary units)
Auxiliary gas pressure: 20
Capillary temperature: 350 °C
Heater temperature: 430 °C