rawDiag

rawDiag facilitates rational method optimization for liquid chromatography coupled to mass spectrometry (LC-MS) by generating diagnostic plots of scan-level metadata tailored for MS operators.

Key Features:

• Diagnostic plot generation: Produces MS operator-tailored diagnostic plots of scan-level metadata for LC-MS method optimization.
• Command-line execution: Runs on the R shell for direct programmatic access.
• Platform-independent processing: Processes data across different computing platforms, with benchmarked performance of 100 raw files in under 3 minutes on current consumer hardware.
• Raw file compatibility: Processes Orbitrap mass spectrometry raw files.

Scientific Applications:

• LC-MS method optimization: Supports rational optimization of liquid chromatography coupled to mass spectrometry methods for bottom-up proteomics.
• Core facility quality control: Enables daily core facility business operations through rapid diagnostic assessment of LC-MS data.

Methodology:

rawDiag is implemented as an R package that parses scan-level metadata from LC-MS raw files and generates diagnostic plots for method optimization assessment.