Raw MS data can be represented visually using the following steps:

1. Load the libraries:

library(mzR)
library(MSnbase)

2. Load the files into objects:

mzxml_file <- file.path(getwd(), "datasets", "ch6", "threonine_i2_e35_pH_tree.mzXML")
ms1 <- openMSfile(mzxml_file)

mzdata_file <- file.path(getwd(), "datasets", "ch6", "HAM004_641fE_14-11-07--Exp1.extracted.mzdata")
ms2 <- openMSfile(mzdata_file)

mzml_file <-  file.path(getwd(), "datasets", "ch6", "MM8.mzML")
ms3 <- openMSfile(mzml_file)

3. View the metadata where available:

runInfo(ms3)

## $scanCount
## [1] 198
## 
## $lowMz
## [1] 95.51765
## 
## $highMz
## [1] 1005.043
## 
## $dStartTime
## [1] 0.486
## 
## $dEndTime
## [1] 66.7818
## 
## $msLevels
## [1] 1
## 
## $startTimeStamp
## [1] "2008-09-01T09:48:37.296+01:00"


sampleInfo(ms1)

## [1] ""

4. Plot the spectra:

msn_exp <- MSnbase::readMSData(mzxml_file)
MSnbase::plot(msn_exp, full = TRUE)
MSnbase::plot(msn_exp[5], full = TRUE)