Journal
JOURNAL OF PROTEOME RESEARCH
Volume 17, Issue 8, Pages 2908-2914Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.8b00173
Keywords
mass spectrometry; R package; multiplatform; method optimization; reproducible research; quality control; visualization
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Funding
- ETH Zurich
- University of Zurich
- Swiss Federal Institute of Technology Zurich
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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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