Plot MS Spectra

Script to read in and plot MS SPectra from Shimadzu MALDI-TOF

Step 1: Read files into dataframes

standardSpectra <- read.table("E3_0001_E3_25-07-18_15-55_0001.txt",header = FALSE, skip = 8)
sampleSpectra <- read.table("E4_0001_E4_25-07-18_15-56_0001.txt", header = FALSE, skip = 8)

#Remove outlier in first row

standardSpectra <- standardSpectra[-1,]
standardSpectra <- standardSpectra[standardSpectra$V1<3000,]
sampleSpectra <- sampleSpectra[-1,]
sampleSpectra <- sampleSpectra[sampleSpectra$V1<3000,]
names(standardSpectra)<-c('mz','intensity')  
names(sampleSpectra)<-c('mz','intensity')

#Tidy Data

library(tidyverse)

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
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## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

sampleSpectra$type <- 'Sample'
standardSpectra$type <- 'Standard'
ms_data <- rbind(sampleSpectra,standardSpectra)
names(ms_data)<-c('mz','intensity','type')

#Simple Scatter Plot

ggplot(ms_data, aes(x = mz,y=intensity))+
  geom_col(aes(colour = type,fill=type))+
  scale_color_manual(values=c("#ffc868","#e5216b"))+
  scale_fill_manual(values=c("#ffc868","#e5216b"))+
  xlab("m/z ratio") + ylab("Millivolts")+
  theme(legend.position="right")

#Simple Line Plot

ggplot(ms_data, aes(x = mz,y=intensity))+
  geom_point(aes(colour = type))+
  scale_color_manual(values=c("#ffc868","#e5216b"))+
  xlab("m/z ratio") + ylab("Millivolts")+
  theme(legend.position="left")

#Facet wrap

ggplot(ms_data, aes(x = mz,y=intensity))+
  geom_col(aes(colour = type ,fill=type))+
  scale_color_manual(values=c("#ffc868","#e5216b"))+
  scale_fill_manual(values=c("#ffc868","#e5216b"))+
  xlab("m/z ratio") + ylab("Millivolts")+
  facet_wrap(~type,nrow=2)

#Find identical peaks

matchSpectra <- merge(standardSpectra,sampleSpectra, by="mz")
write.csv(matchSpectra,"matchSpectra.csv")