LC-MS plant metabolomics (Poaceae)

Knowledge graph centered on LC-MS plant metabolomics (Poaceae) with 62 nodes and 121 connections. Top connected: Rocky Mountain Biological Laboratory, Gothic, East River, Climate Change Impacts, Festuca thurberi.

Method synopsis

Extraction of plant metabolites using methanol/acetonitrile/water solvent followed by liquid chromatography-mass spectrometry analysis. Characterizes plant metabolomic profiles for correlation with fungal communities.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Warming disrupts plant–fungal endophyte symbiosis more severely in leaves than roots (2025), Global Change Biology. Implementations in other papers (listed below) may differ.

1. Prepare samples for metabolomics
   For RMBL and Kessler experiments, plant leaf and root samples (100 mg) were weighed into 1.5 mL centrifuge tubes. Added 1.3 mL extraction solvent (40:40:20 HPLC grade methanol, acetonitrile, water with 0.1% formic acid) pre-chilled to 4°C. Samples vortexed, extracted for 20 min at 4°C while shaken, centrifuged for 5 min (16.1 rcf) at 4°C. Supernatant transferred and extraction repeated twice more. Final supernatant centrifuged and 1.2 mL transferred to vials, dried under N₂ stream, resuspended in 300 μL sterile water.
   Quantities: 100 mg plant tissue, 1.3 mL extraction solvent, final 300 μL resuspension volumeDuration: 20 min extraction at 4°C, repeated 3 times total, 5 min centrifugation stepsConditions: 4°C extraction temperature, orbital shaking
   Equipment: centrifuge tubes, HPLC grade solvents, vortex, orbital shaker, centrifuge, N₂ stream
2. Mass spectrometry analysis
   Samples analyzed with 10 μL injection through Synergi 2.5 μm reverse-phase Hydro-RP 100, 100 x 2.00 mm LC column at 25°C. Eluted into Exactive™ Plus Orbitrap Mass Spectrometer through 0.1 mm internal diameter fused silica capillary tube. Full scan mode with negative ionization, window 85-1000 m/z, spray voltage 3 kV, nitrogen sheath gas 10 psi flow rate, capillary temperature 320°C, AGC target 3e6, resolution 140,000, scan window 85-800 m/z (0-9 min) and 110-1000 m/z (9-25 min).
   Quantities: 10 μL injection volume, 85-1000 m/z mass range, 3 kV spray voltage, 10 psi gas flow, 320°C capillary temperatureDuration: 25 minute gradient run per sampleConditions: 25°C column temperature, negative ionization mode

Typical Equipment

• HPLC grade solvents
• Synergi 2.5 μm reverse-phase Hydro-RP column
• Exactive™ Plus Orbitrap Mass Spectrometer

Output Measurements

• metabolite abundance profiles

Papers Using This Protocol (1)

Species Studied With This Protocol

Places Where Used