Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

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Method synopsis

High-resolution mass spectrometry analysis using Fourier Transform Ion Cyclotron Resonance to characterize the molecular composition of organic matter in different chemical extractions.

Synthesized from method descriptions across 4 papers 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 — Molecular diversity of dissolved organic matter reflects macroecological patterns in river networks (2025), Scientific Reports. Implementations in other papers (listed below) may differ.

1. Water sample collection
   Samples were collected, extracted, and analysed per the WHONDRS Consortium protocols. Surface water and sediment samples were collected across 97 sites and 9 countries for 6 weeks between July and August 2019 by the WHONDRS network.
   Quantities: 97 sites across 9 countries, 54 sites used in final analysisDuration: 6 weeks between July and August 2019Conditions: Surface river waters during summer sampling period
   Equipment: WHONDRS Consortium sampling protocols
2. Mass spectrometry analysis
   Surface water and sediment extracts were analyzed on a 12 Tesla Bruker SolariX Fourier transform ion cyclotron mass spectrometer at the Environmental Molecular Sciences Laboratory. Negative mode spectra were collected from 100 to 900 m/z with appropriate ion accumulation times for each sample type. Raw spectra were processed using a signal-to-noise ratio threshold of 7.
   Quantities: Resolution: 220 K at 481.185 m/z, mass range 100-900 m/zDuration: Not specifiedConditions: Negative mode spectra collection
   Equipment: 12 Tesla Bruker SolariX Fourier transform ion cyclotron mass spectrometer, Environmental Molecular Sciences Laboratory
3. Molecular formulae assignment
   Molecular formulae were assigned using established software pipelines including Formularity and ftmsRanalysis. Quality control measures included removing peaks outside the 200-900 m/z confidence range. Formulae were classified into compound class based on elemental ratios: lignin-like (O/C: 0.1-0.7, H/C: 0.6-1.2), lipid-like (O/C: 0-0.3, H/C: 1.5-2.5), protein-like (N > 0, O/C: 0.2-0.6, H/C: 1.5-2.2), carbohydrate-like (O/C: 0.7-1.2, H/C: 1.5-2.2), and condensed aromatic formulae (O/C: 0-0.7, H/C: 0.2-0.7).

Typical Equipment

• 12 T Bruker SolarX FTICR spectrometer
• bond elute PPL cartridges
• HPLC grade methanol

Output Measurements

• molecular formulas
• NOSC
• molecular weight
• compound classes

Papers Using This Protocol (4)

Species Studied With This Protocol

Places Where Used