rawDiag: An R Package Supporting Rational LC-MS Method Optimization for Bottom-up Proteomics.
Christian TrachselChristian PanseTobias KockmannWitold E WolskiJonas GrossmannRalph SchlapbachPublished in: Journal of proteome research (2018)
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.
Keyphrases
- mass spectrometry
- liquid chromatography
- high resolution mass spectrometry
- gas chromatography
- tandem mass spectrometry
- high performance liquid chromatography
- capillary electrophoresis
- high resolution
- computed tomography
- high throughput
- physical activity
- simultaneous determination
- solid phase extraction
- magnetic resonance imaging
- ms ms
- single cell