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