calc_eval_params: Calculate UME Evaluation Parameters

In ume: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

Calculate UME Evaluation Parameters

Description

This function calculates and adds several evaluation parameters as additional columns to the mfd data table. These parameters are essential for evaluating the molecular structure and isotopic distribution, enabling further analysis. For a detailed description of the output table, see help(mf_data_demo).

Usage

calc_eval_params(mfd, verbose = FALSE, ...)

Arguments

mfd	data.table with molecular formula data as derived from ume::assign_formulas. Column names of elements/isotopes must match names in the isotope column of ume::masses; values are integers representing counts per formula.
verbose	logical; if TRUE, show progress messages.
...	Additional arguments passed to methods.

Value

The original data.table mfd with additional evaluation columns:

nm

Nominal molecular mass: Calculated if not already present.

dbe)

Double Bond Equivalent (measure of unsaturation).

kmd

Kendrick mass defect for CH4 versus O exchange.

O/C, H/C, N/C, S/C)

Element ratios for a molecular formula.

nsp_type, snp_check

Types of combinations of N, S, and P atoms in a formula.

⁠nosc``}{Weighted average nominal oxidation state of carbon.} \item{⁠delG0_Cox⁠}{Weighted average Gibbs free energy (Cox) in kJ/mol.} \item{⁠ai⁠}{Aromaticity index.} \item{⁠ppm_filt'

A mass accuracy threshold calculated for each spectrum.

Author(s)

Boris P. Koch

References

Hughey C.A., Hendrickson C.L., Rodgers R.P., Marshall A.G., Qian K.N. (2001). Kendrick mass defect spectrum: A compact visual analysis for ultrahigh-resolution broadband mass spectra. Analytical Chemistry, 73, 4676-4681. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/ac010560w")}

Koch B.P., Dittmar T. (2006). From mass to structure: an aromaticity index for high-resolution mass data of natural organic matter. Rapid Communications in Mass Spectrometry, 20, 926-932. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/rcm.2386")}

LaRowe D.E., Van Cappellen P. (2011). Degradation of natural organic matter: A thermodynamic analysis. Geochimica et Cosmochimica Acta, 75, 2030-2042. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.gca.2011.01.020")}

See Also

Other Formula assignment: add_known_mf(), check_formula_library(), eval_isotopes(), ume_assign_formulas()

Other calculations: calc_data_summary(), calc_dbe(), calc_exact_mass(), calc_ideg(), calc_ma(), calc_neutral_mass(), calc_nm(), calc_norm_int(), calc_number_assignment(), calc_number_occurrence(), calc_recalibrate_ms()

Examples

# Example usage with a demo molecular formula dataset
mfd_with_params <- calc_eval_params(mfd = mf_data_demo, verbose = TRUE)

ume documentation built on Dec. 13, 2025, 1:06 a.m.