calibrateMW: calibrate Molecular Weight

In CCprofiler/CCprofiler: Complex feature detection using SEC protein chromatograms.

Description

Establish connectivity between fraction number and apparent Molecular Weight(MW) (in kDa). Many fractionation based PCP expeiments will have a set of standard proteins with known MW spiked in the samples. These reference proteins can be used in this function to calibrate the corresponding MW of every fraction. While this is not neccesary for downstream analysis, it is recommended if standard proteins are available, since it facilitates the process of drawing biological conclusions.

Usage

calibrateMW(calibration_table, plot = TRUE, PDF = FALSE)

Arguments

calibration_table	A table with protein standards, file or R data.table. Columns: std_weights_kDa Numeric, the MW of the standard proteins. std_elu_fractions Numeric, the fraction numbers where these standard proteins eluted. For an example see exampleCalibrationTable.
plot	Logical, whether to plot calibration curve. Defaults to TRUE.
PDF	Logical, whether to produce a PDF file in the working directory. Defaults to FALSE.

Details

The function uses a standard lm() of the form log2(MW) ~ fraction. Therefore, the fractionation technique is required to have a log-linear relationship between fraction and molecular weight (True for e.g. standard SEC methods). The estimated slope and intersect of the model are then used for the returned calibration functions.

Value

List of two functions: MWtoFraction and FractionToMW.

Examples

## Load example data
standardProteinTable <- exampleCalibrationTable
## Regress the standard proteins against their elution fractions
calibrationFunctions <- calibrateMW(standardProteinTable,
                                       plot = TRUE,
                                       PDF = FALSE)
# The provided plot can be used for quality assessment. The points represent the
# standard proteins and should agree with the model (solid line))

## The molecular weight (in kDa) of an arbitrary fraction can now be calculated.
calibrationFunctions$FractionToMW(14)

## Arbitrary MWs (in kDa) can also be converted to fraction numbers
calibrationFunctions$MWtoFraction(3020) # i.e. 3020 kDa

CCprofiler/CCprofiler documentation built on May 19, 2021, 7:40 p.m.