PTXQC (version 1.0.4)

plot_MBRAlign: Plot MaxQuant Match-between-runs alignment performance.

Description

The plots shows the correction function applied by MaxQuant, and the residual RT (ideally 0) of each peptide to its reference. Uncalibrated peptides are shown in red, calibrated ones in green. The MaxQuant RT correction which was applied prior is shown in blue. The range of this function can give hints if the allowed RT search window (20min by default) is sufficient or if MaxQuant should be re-run with more tolerant settings.

Usage

plot_MBRAlign(data, y_lim, title_sub, match_tol)

Arguments

data

A data.frame with columns as described above

y_lim

Plot range of y-axis

title_sub

Subtitle

match_tol

Maximal residual RT delta to reference (usually ~1 min)

Value

GGplot object

Details

The input is a data.frame with columns 'calibrated.retention.time' - resulting (hopefully) calibratated RT after MQ-recal (the X-axis of the plot) 'retention.time.calibration' - delta applied by MaxQuant 'rtdiff' - remaining RT diff to reference peptide of the same sequence 'RTdiff_in' - is the feature aligned (within 'match_tol')? 'fc.raw.file_ext' - raw file where each row represents one peptide whose RT was corrected by MaxQuant.

Examples

# NOT RUN {
 data = data.frame(fc.raw.file_ext = "file A", ## more than one would be possible
                   calibrated.retention.time = c(20:100), 
                   retention.time.calibration = 6 + sin((20:100)/10))
 data$rtdiff = rnorm(nrow(data))
 data$RTdiff_in = c("green", "red")[1 + (abs(data$rtdiff) > 0.7)]
 
 plot_MBRAlign(data, c(-10, 10), "fancy subtitle", 0.7)

# }