Converting MS formats to move data between tools can be done using the following steps:

1. Load the library and import the source data file:

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

2. Extract the header and peak data:

header_info <- header(mzdata)
peak_data_list <- spectra(mzdata)

3. Write the data into a new format file:

writeMSData(peak_data_list, 
 file.path(getwd(), "datasets", "ch6", "out.mz"), 
 header = header_info, 
 outformat = "mzml", 
 rtime_seconds = TRUE 
)