calculateKendrickMass: Kendrick mass defects

In rformassspectrometry/MetaboCoreUtils: Core Utils for Metabolomics Data

Kendrick mass defects

Description

Kendrick mass defect analysis is a way to analyze high-resolution MS data in order to identify homologous series. The Kendrick mass (KM) is calculated by choosing a specific molecular fragment (e.g. CH2) and settings its mass to an integer mass. In case of CH2 the mass of 14.01565 would be set to 14.The Kendrick mass defect (KMD) is defined as the difference between the KM and the nominial (integer) KM. All molecules of homologoues series, e.g. only differing in the number of CH2, will have an identical KMD. In an additional step the KMD can be referenced to the mass defect of specific lipid backbone and by this normalize values to the referenced KMD (RKMD). This leads to values of 0 for saturated species or -1, -2, -3, etc for unsaturated species.

Available functoins are:

• calculateKm: calculates the Kendrick mass from an exact mass for a specific molecular fragment, e.g. "CH2".

• calculateKmd: calculates the Kendrick mass defect from an exact mass for a specific molecular fragment, e.g. "CH2".

• calculateRkmd: calculates the referenced Kendrick mass defect from an exact mass for a specific molecular fragment, e.g. "CH2", and a reference KMD.

• isRkmd: Checks if a calculated RKMD falls within a specific error range around an negative integer corresponding the number of double bonds, in case of CH2 as fragment.

Usage

calculateKm(x, fragment = 14/14.01565)

calculateKmd(x, fragment = 14/14.01565)

calculateRkmd(x, fragment = 14/14.01565, rkmd = 0.749206)

isRkmd(x, rkmdTolerance = 0.1)

Arguments

x	numeric with exact masses or calculated RKMDs in case of isRkmd.
fragment	numeric(1) or character(1) corresponding factor or molecular formula of molecular fragment, e.g. 14 / 14.01565 or "CH2" for CH2.
rkmd	numeric(1) KMD used for referencing of KMDs.
rkmdTolerance	numeric(1) Tolerance to check if RKMD fall around a negative integer corresponding to the number of double bonds

Value

numeric or boolean. All functions, except isRkmd return a numeric with same length as the input corresponding to the KM, KMD or RMKD. isRkmd returns a logical with TRUE or FALSE indicating if the RKMD falls within a specific range around a negative integer corresponding to the number of double bonds.

Author(s)

Michael Witting

Examples

calculateKm(760.5851)

calculateKmd(760.5851)

calculateRkmd(760.5851, rkmd = 0.749206)

isRkmd(calculateRkmd(760.5851, rkmd = 0.749206))

rformassspectrometry/MetaboCoreUtils documentation built on Oct. 2, 2024, 5:13 a.m.