10  Convert data using proteowizard

10.1 Install Proteowizard

Proteowizard only supports Windows OS. So if you don’t use Windows OS, consider massconverter.

Download Proteowizard and install it.

10.2 Data preparation

Please place the raw data in one folder according to MS1 and MS2. Then you can convert them using Proteowizard package.

10.3 Convert MS1 data to mzXML format data

Just convert data into mzXML format data according to the parameters below:

10.4 Convert MS2 data to mzXML or mgf format data

Just convert data into mzXML or mgf format data according to the parameters below:

10.5 Session information

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Singapore
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] htmlwidgets_1.6.4 compiler_4.4.1    fastmap_1.2.0     cli_3.6.3        
 [5] tools_4.4.1       htmltools_0.5.8.1 rstudioapi_0.17.1 rmarkdown_2.29   
 [9] knitr_1.49        jsonlite_1.8.9    xfun_0.52         digest_0.6.37    
[13] rlang_1.1.4       evaluate_1.0.1