Plot MS Spectra

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

#Step 1: Read files into dataframes

standardSpectra <- read.table('G3_0001_G3_25-07-18_15-50_0001.txt',
                              header = FALSE, skip= 8)  
sampleSpectra <- read.table('G4_0001_G4_25-07-18_15-51_0001.txt', 
                            header = FALSE, skip= 8)

#Remove the outlier in the first row ##Rename column titles

standardSpectra <- standardSpectra [-c(1, 22), ]
sampleSpectra <- sampleSpectra [-c(1, 48),]
names(standardSpectra) <- c('m_z', 'intensity')
names(sampleSpectra) <- c('m_z', 'intensity')

#Tidy data

library(tidyverse)

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr     1.1.4     ✔ readr     2.1.5
## ✔ forcats   1.0.0     ✔ stringr   1.5.1
## ✔ ggplot2   3.5.2     ✔ tibble    3.3.0
## ✔ lubridate 1.9.4     ✔ tidyr     1.3.1
## ✔ purrr     1.1.0     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## 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')

#Create Scatter 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")

#Create Column 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")

#Find Peaks with Identical M/Z Ratio ##Write .csv final

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