mobilityTransform: Effective mobility scale transformation of CE-MS data

In LiesaSalzer/MobilityTransformR: Effective mobility scale transformation of CE-MS(/MS) data

Effective mobility scale transformation of CE-MS data

Description

mobilityTransform performs effective mobility scale transformation of CE(-MS) data, which is used to overcome variations of the migration times, caused by differences in the Electroosmotic Flow (EOF) between different runs. In order to monitor the EOF and perform the transformation, neutral or charged EOF markers are spiked into the sample before analysis. The information of the EOF markers (migration time and effective mobility) will be then used to perform the effective mobility transformation of the migration time scale.

For the transformation, either one mobility marker or both can be used. If a single marker is used, either a neutral EOF marker, or charged marker with its corresponding mobilities (0 for the neutral marker) must be provided, along with the applied voltage U, and the total capillary length L. If two markers are used, both a neutral EOF marker and a charged marker including their corresponding mobility must be provided. Additionally, field ramping delays can be included by tR, which will result in more precise effective mobility values.

Currently, mobilityTransform supports numeric vectors of migration times as input, Spectra-objects or MSnOnDiskExp-objects. mobilityTransform is a method that used different functions to convert CE-MS data, depending on the input class. Following functions will be applied depending on the input class:

 `.transformNumeric`: performs effective mobility scale
 transformation of a `numeric` migration time vector as input. This
 can be used to transform a row of migration times or a single
 value. This function will return a `numeric`


 `.transformSpectra` performs effective mobility scale
 transformation of the migration time scale within a `Spectra`
 object. This function will return a `Spectra` object with
 effective mobility scale


 `.transformOnDiskMSnExp` performs effective mobility scale
 transformation of the migration time scale within an `OnDiskMSnExp`
 object.
 Since `OnDiskMSnExp` can store multiple files, it is also possible
 to perform the transformation of multiple files. Hence,
 `.transformOnDiskMSnExp` requires the `marker` `data.frame` to
 have an additional column "fileIdx" that stores the file Index of
 the migration time of all markers.

Usage

mobilityTransform(x, marker, tR = 0, U = numeric(), L = numeric())

Arguments

x	numeric migration time vector, Spectra -object, or MSnOnDiskExp- object that serves as input file to perform the effective mobility transformation. The respective migration time scale should be in seconds(!).
marker	data.frame containing minimum two columns, where one holds the determined migration time in minutes (here referred to as "rtime") of the EOF marker in the same run in which the migration time is going to be transformed and the other column the respective mobility ("mobility") of the EOF markers. Each row hold the values for one EOF marker. If OnDiskMSnExp is used in x, a third column "fileIdx" is required, that stores the file Index. One or two entries are required per file for the transformation and depending on the number of entries the transformation will be performed either on one or both markers.
tR	numeric a single value that defines the time (in minutes) of the electrical field ramp. The default is 0.
U	numeric a single value that defines the voltage (in kV) applied. Note that for reversed polarity CE mode a negative value is needed.
L	numeric a single value that defines the total length (in mm) of the capillary that was used for CE(-MS) analysis.

Value

The same class as the input class will be returned, i.e. if a numeric is used as input a numeric that represents effective mobility will be returned. If a Spectra-Object is the input, also a Spectra-Object with transformed mobility scale will be returned. The same applies for MSnOnDiskExp-objects. The respective unit for the effective mobility is mm^2 / (kV * min)

Author(s)

Liesa Salzer

Examples

rtime <- c(10, 20, 30, 40, 50, 60, 70, 80, 90, 100)
marker <- data.frame(
    markerID = c("marker1", "marker2"),
    rtime = c(20, 80),
    mobility = c(0, 2000)
)
mobilityTransform(x = rtime, marker = marker)

LiesaSalzer/MobilityTransformR documentation built on April 1, 2022, 6:24 p.m.