Fourier transform ion cyclotron resonance (FT ICR) mass spectrometry data
Creators: name: Xia, Mingming
name: Liu, Ming
Publisher: name: Zenodo
Year: 2025
Subjects: dissolved organic matter
FT-ICR MS
Molecular transformation potential

description: Understanding dissolved organic matter (DOM) transformation is crucial for comprehending soil biogeochemical cycling. However, the extent that soil microbes mediate DOM transformation at the molecular level, and whether this is regulated by soil management practices such as fertilization remain largely unknown. We investigated soil DOM transformations under long-term fertilization using Fourier-transform ion cyclotron resonance mass spectrometry, high-throughput sequencing, and machine learning. Fertilization greatly promoted transformation potential of DOM molecules. Notably, organic fertilization increased the mean transformation number of DOM molecules by 260% compared to no-fertilization, while chemical fertilization increased it by 193.33%. Machine learning indicated that intrinsic DOM molecular characteristics (aromaticity index, oxygen/carbon, and hydrogen/carbon ratios) could predict transformation potential, especially for medium- or low-transformation-potential molecules. However, high-transformation-potential DOM molecules were more influenced by soil microorganisms that contributed to DOM transformation (e.g., Desulfobacterota). Our study provides a parameter to characterize potential transformation capacity of DOM molecules, the effects of different fertilization treatments on this potential, and highlights microbial contributions to molecular transformation processes, identifying the key microbial groups.
description: Funding provided by: National Natural Science Foundation of ChinaROR ID: https://ror.org/01h0zpd94Award Number: 42177294
Funding provided by: National Natural Science Foundation of ChinaROR ID: https://ror.org/01h0zpd94Award Number: 42267046
Funding provided by: National Natural Science Foundation of ChinaROR ID: https://ror.org/01h0zpd94Award Number: 42167049
Funding provided by: China Agriculture Research Systems of MOF and MARACrossref Funder Registry ID: Award Number: CARS-22
Funding provided by: the Key Research and Development Program of Jiangxi ProvinceCrossref Funder Registry ID: Award Number: 20212BBF63007
description: This data includes Fourier high resolution mass spectrometry data of dissolved organic matter (DOM) molecules under different fertilization treatmentsThe DOM was extracted from soil samples (6 g) using a soil-to-water ratio of 1:5 and ultrapure water. Ultrapure water used for all experiments and solutions had a resistivity of 18.2 MΩ·cm at 25℃ and a total organic carbon content lower than 5 ppb. The mixture was subjected to shaking for 12 h at room temperature on a horizontal shaker. Subsequently, the solutions were centrifuged at 1200 × g for 10 min and filtered through a 0.45 μm membrane filter. For clean-up, HPLC methanol (10 mL) and acidified ultrapure water (10 mL, pH 2) were passed through PPL cartridges (Agilent Technologies, Santa Clara, CA, USA). The DOM solution was then loaded onto the PPL cartridges by gravity flow. Following that, DOM was collected from the cartridges using 10 mL of methanol (HPLC grade; Merck, Darmstadt, Germany). The collected DOM eluates were stored at −20°C in darkness prior to electrospray ionization FT-ICR-MS analysis.

A deuterated octadecanoic acid compound was added to the samples as an internal standard, with a dosage of 15 μL (5 × 10−7 mol L−1) per milliliter of the sample. The FT-ICR MS instrument (Bruker, Billerica, MA, USA) utilized a 9.4 Tesla actively shielded superconducting magnet in negative-ion mode. Each sample was injected into the ESI source at a flow rate of 180 μL h−1 using a syringe pump. The polarization voltage was set at 4.0 kV, while the capillary column introduction and outlet voltage were 4.5 kV and 320 V, respectively. Ions were accumulated in the hexapole for 0.001 s before being transferred to the ICR cell. The mass-to-charge ratio (m/z) range analyzed was 150–800 Da. A time-domain signal acquisition with a 4 M word size was selected. Signal-to-noise ratio and dynamic range were enhanced through the accumulation of 128 domain FT-ICR transients.

The data obtained were processed using the Data Analysis software (Bruker Daltonics version 4.2). The raw spectra were converted into a list of mass-to-charge ratio (m/z) values using the FTMS peak picker algorithm, with a signal-to-noise (S/N) threshold of 6 and an absolute intensity threshold of 100. To minimize cumulative errors, all peaks from the entire dataset were aligned to each other, ensuring elimination of potential mass shifts. The molecular formulas of the identified mass peaks were determined using custom software designed for this purpose. The assigned molecular formulas were classified into distinct categories based on the ratios of oxygen to carbon (O/C) and hydrogen to carbon (H/C) as follows: lipids for H/C = 1.5–2.0, O/C = 0–0.3; aliphatic/proteins for H/C = 1.5–2.2, O/C = 0.3–0.67; lignin/CRAM-like for H/C = 0.7–1.5, O/C = 0.1–0.67; carbohydrates for H/C = 1.5–2.4, O/C = 0.67–1.2; unsaturated hydrocarbons for H/C =0.7–1.5, O/C = 0–0.1; aromatic structures for H/C = 0.2–0.7, O/C =0–0.67; and tannin for H/C = 0.6–1.5, O/C = 0.67–1.0