foo <- (data.table::fread('./evidence.txt', select = c('Retention time','Modified sequence', 'Charge', 'Experiment')))
foo2 <- data.matrix((tidyr::spread(foo[!isdup], Experiment, `Retention time`))[,3:14])
foo_numnas <- rowSums(!is.na(foo2))
foo2 <- foo2[foo_numnas > 1,]
foo2 <- cbind(foo2-rowMeans((foo2), na.rm = TRUE) ,rowMeans((foo2), na.rm = TRUE))
colnames(foo2)[ncol(foo2)] <- 'MeanRT'
tidyRTs <- (tidyr::gather(as.data.frame(foo2), -MeanRT, key = 'variable', val = 'value'))

ggplot2::ggplot(tidyRTs, ggplot2::aes(x = MeanRT, y = value)) +
    ggplot2::geom_bin2d() +
    ggplot2::facet_wrap(. ~ variable) +
    ggplot2::lims(y = c(-3,3))