add_known_mf: Add metainformation derived from ume::known_mf

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

Add metainformation derived from ume::known_mf

Description

Join molecular formula data and metadata about known formulas (e.g. annotate carboxylic-rich alicyclic molecules (CRAM)). The name of the molecular formula column will be set to "mf".

Usage

add_known_mf(mfd, mf_col = "mf", known_mf = ume::known_mf, ...)

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.
mf_col	Name of the column in mfd that has the molecular formula information (default: "mf"). Formulas have upper case element symbols and elements in the formula are ordered according to the Hill system.
known_mf	data.table with known molecular formulas (ume::known_mf).
...	Additional arguments passed to methods.

Value

A data.table containing additional columns having information on formula categories

Author(s)

Boris P. Koch

References

CRAM Hertkorn N., Benner R., Frommberger M., Schmitt-Kopplin P., Witt M., Kaiser K., Kettrup A., Hedges J.I. (2006). Characterization of a major refractory component of marine dissolved organic matter. Geochimica et Cosmochimica Acta, 70, 2990-3010. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.gca.2006.03.021")} Surfactants Lechtenfeld O.J., Koch B.P., Gasparovic B., Frka S., Witt M., Kattner G. (2013). The influence of salinity on the molecular and optical properties of surface microlayers in a karstic estuary. Marine Chemistry, 150, 25-38. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.marchem.2013.01.006")}

Ideg Flerus R., Lechtenfeld O.J., Koch B.P., McCallister S.L., Schmitt-Kopplin P., Benner R., Kaiser K., Kattner G. (2012). A molecular perspective on the ageing of marine dissolved organic matter. Biogeosciences, 9, 1935-1955. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5194/bg-9-1935-2012")}

iTerr Medeiros P.M., Seidel M., Niggemann J., Spencer R.G.M., Hernes P.J., Yager P.L., Miller W.L., Dittmar T., Hansell D.A. (2016). A novel molecular approach for tracing terrigenous dissolved organic matter into the deep ocean. Global Biogeochemical Cycles, 30, 689-699. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/2015gb005320")}

See Also

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

Examples

add_known_mf(mfd = mf_data_demo)

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