VDAP (version 2.0.0)

QCKd: Quality Control of Peptides Based on Reproducibility and Kd

Description

Filter out peptides based on reproducibility between replicate concentrations and relative dissociation constants (Kd). Peptides must have a signal ratio between 0.5 and 2.0. A second reference file may be loaded with the same peptides referenced against another sample. Peptides are then compared based upon relative Kd value which must be at least one log10 apart.

Usage

QCKd(File1, File2 = NULL, Kd = FALSE, QC = TRUE, ColSet1 = NULL,
ColSet2 = NULL, ColSet3 = NULL)

Arguments

File1

An R object, usually a data.frame generally created by the function FLoad()

File2

An R object, usually a data.frame generally created by the function FLoad()

Kd

A logical value, if Kd = TRUE then peptides will be filtered by Kd against the argument File2

QC

A logical value, if QC = TRUE then peptides will be filtered by ratios of signal between replicates. Ratios must be between 0.5 to 2.0 to remain in the dataset.

ColSet1

A sequence value, represents the two columns that are replicates at a single concentration. Peptides must fit QC criteria in all given ColSets to remain in the dataset. ColSets may be omitted if less than three concentrations are to be compared. Ex: 2:3

ColSet2

A sequence value, represents the two columns that are replicates at a single concentration. Peptides must fit QC criteria in all given ColSets to remain in the dataset. ColSets may be omitted if less than three concentrations are to be compared. Ex: 6:7

ColSet3

A sequence value, represents the two columns that are replicates at a single concentration. Peptides must fit QC criteria in all given ColSets to remain in the dataset. ColSets may be omitted if less than three concentrations are to be compared. Ex: 4:5

Value

A data.frame will be returned with peptides filtered out that do not meet the given criteria for either the QC or Kd filters.

Details

Either the QC or Kd filter may be applied by itself of both simultaneously.

Examples

protEx.QCKd <- data.frame(Peptides = c("PWRGPWARVGSG","GYNRVGQGSG","PNGYRSGVKGSG","GSG"),
Length = c(12,10,12,3),Charge = c(2,1,2,0),Kd = c(0.2572361,2.8239730,3.3911868,281.3058),
C_6uM = c(65011.48,47462.24,24778,2613.03),C_6uM2 = c(62637.81,20723.85,21313.67,2300.216))

## All peptides filtered out due to same Kd value between files ##

QCKdEx <- QCKd(protEx.QCKd, protEx.QCKd,Kd = TRUE, QC = TRUE, ColSet1 = 5:6)

## QC control only ##

QCKdEx <- QCKd(protEx.QCKd, QC = TRUE, ColSet1 = 5:6)