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bioRxiv · 10.1101/304485

rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics

Trachsel, C.·Panse, C.·Kockmann, T.·Wolski, W. E.·Grossmann, J.·Schlapbach, R.
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Abstract

Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) is a non-trivial 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 R package and can be executed on the command line, or through a graphical user interface (GUI) for less experienced users. The code runs platform independent and can process a hundred raw files in less than three minutes on current consumer hardware as we show by our benchmark. In order to demonstrate the functionality of our package, we included a real-world example taken from our daily core facility business.

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Trachsel, C., Panse, C., Kockmann, T., Wolski, W. E., Grossmann, J., Schlapbach, R.. 2018-04-24. rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics. https://doi.org/10.1101/304485

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