7   Convert raw data to mzXML/mgf

 

TidyMass packages:

Data preparation

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

Proteowizard

Convert MS1 data to mzXML format data 🔗︎

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

Convert MS2 data to mzXML or mgf format data 🔗︎

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

Convert data using massconverter

massconverter is a package in tidymass project which can be used to convert mass spectrometry raw data based on docker image of pwid. See more information here.

More information can be found here.

Session information

sessionInfo()
#> R version 4.1.2 (2021-11-01)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] magrittr_2.0.2
#> 
#> loaded via a namespace (and not attached):
#>  [1] bookdown_0.24   here_1.0.1      rprojroot_2.0.2 digest_0.6.29  
#>  [5] R6_2.5.1        jsonlite_1.7.3  evaluate_0.15   blogdown_1.7   
#>  [9] rlang_1.0.1     stringi_1.7.6   cli_3.2.0       rstudioapi_0.13
#> [13] jquerylib_0.1.4 bslib_0.3.1     rmarkdown_2.11  tools_4.1.2    
#> [17] stringr_1.4.0   xfun_0.29       yaml_2.3.4      fastmap_1.1.0  
#> [21] compiler_4.1.2  htmltools_0.5.2 knitr_1.37      sass_0.4.0