getwd()
#> [1] "/Users/xiaotaoshen/tidymass/tidymass-website/content/docs/chapter3"
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 4.3.0 (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