getwd()
#> [1] "/Users/xiaotaoshen/tidymass/tidymass-website/content/docs/chapter3"
Install Proteowizard
Proteowizard only supports Windows OS. So if you don’t use Windows OS, consider massconverter.
Download Proteowizard and install it.
Data preparation
Please place the raw data in one folder according to MS1 and MS2. Then you can convert them using Proteowizard package.
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:
Session information
sessionInfo()
#> R version 4.3.0 (2023-04-21)
#> Platform: x86_64-apple-darwin20 (64-bit)
#> Running under: macOS Ventura 13.5.1
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
#>
#> 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: America/Los_Angeles
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> loaded via a namespace (and not attached):
#> [1] digest_0.6.31 R6_2.5.1 codetools_0.2-19 bookdown_0.34
#> [5] fastmap_1.1.1 xfun_0.39 blogdown_1.18.1 cachem_1.0.8
#> [9] knitr_1.43 htmltools_0.5.5 rmarkdown_2.22 cli_3.6.1
#> [13] sass_0.4.6 jquerylib_0.1.4 compiler_4.3.0 rprojroot_2.0.3
#> [17] here_1.0.1 rstudioapi_0.14 tools_4.3.0 evaluate_0.21
#> [21] bslib_0.5.0 yaml_2.3.7 jsonlite_1.8.5 rlang_1.1.1