Plot Shimadzu MALDI-TOF Spetra

Import data that was saved as ASCII in Shimadzu software

f2 <- read.csv('F2.csv', header = FALSE)
f3 <- read.csv('F3.csv', header = FALSE)

f2$V3 <- 'Standard Digest'
f3$V3 <- 'Experimental Digest'
f2 <- f2[,1:3]
f3 <- f3[,1:3]
ms_data <- rbind(f2,f3)
names(ms_data) <-c('mz','intensity','sample')

#create a basic scatter plot with points

library(tidyverse)

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ggplot(ms_data, aes(x=mz, y=intensity))+
  geom_point(aes(colour = sample))+
  scale_colour_manual(values=c("#fdc400", "#1957fb"))+
  xlab("m/z ratio")+ylab("Millivolts")+
  labs(fill="sample")+
  theme(legend.position = "left")

#create a column plot to compare samples

ggplot(ms_data, aes(x=mz, y=intensity))+
  geom_col(aes(colour = sample, fill=sample))+
  scale_color_manual(values=c("#fdc400", "#1957fb"))+
  scale_fill_manual(values=c("#fdc400", "#1957fb"))+
  xlab("m/z ratio")+ylab("Millivolts")+
  theme(legend.position = "right")

#find peaks with identical m/z

matchSpectra <- merge(f2,f3, by="V1")
write.csv(matchSpectra, "matchSpectra.csv")