rawDiag: An R Package Supporting Rational LC–MS Method Optimization for Bottom-up Proteomics
2018
Trachsel, Christian | Panse, Christian | Kockmann, Tobias | Wolski, Witold E. | Grossmann, Jonas | Schlapbach, Ralph
Optimizing methods for liquid chromatography coupled to mass spectrometry (LC–MS) is a nontrivial task. Here we present rawDiag, a software tool supporting rational method optimization by providing MS operator-tailored diagnostic plots of scan-level metadata. rawDiag is implemented as an R package and can be executed on the R command line or through a graphical user interface (GUI) for less experienced users. The code runs platform-independent and can process 100 raw files in <3 min on current consumer hardware, as we show in our benchmark. As a demonstration of the functionality of our package we include a real-world example taken from our daily core facility business.
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