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Convert raw data to mzXML/mgf

Xiaotao Shen (https://www.shenxt.info/)

Created on 2021-12-04 and updated on 2022-03-21

data_convert.Rmd

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 inforamtion can be found here.

Session information 

sessionInfo()
#> R Under development (unstable) (2022-01-11 r81473)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur/Monterey 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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     
#> 
#> loaded via a namespace (and not attached):
#>  [1] rprojroot_2.0.2   digest_0.6.29     crayon_1.4.2      R6_2.5.1         
#>  [5] jsonlite_1.7.2    magrittr_2.0.1    evaluate_0.14     stringi_1.7.6    
#>  [9] rlang_0.4.12      cachem_1.0.6      fs_1.5.2          jquerylib_0.1.4  
#> [13] bslib_0.3.1       ragg_1.2.1        rmarkdown_2.11    pkgdown_2.0.1    
#> [17] textshaping_0.3.6 desc_1.4.0        tools_4.2.0       stringr_1.4.0    
#> [21] purrr_0.3.4       yaml_2.2.1        xfun_0.29         fastmap_1.1.0    
#> [25] compiler_4.2.0    systemfonts_1.0.3 memoise_2.0.1     htmltools_0.5.2  
#> [29] knitr_1.37        sass_0.4.0