rawR

rawR: R package for direct access to Thermo Fisher Scientific mass spectrometry raw files

rawR provides OS-independent access to Thermo Fisher Scientific raw mass spectrometry (MS) files within R by wrapping the RawFileReader .NET assembly and enabling extraction and analysis of complete spectral data, including spectra and chromatograms, as S3 objects.

Key Features:

• Complete Spectral Data Access: Extracts full spectral data, including spectra and chromatograms, from Thermo Fisher Scientific raw files and represents them as S3 objects in R.
• Vendor API Wrapping: Wraps the RawFileReader .NET assembly to access MS raw file data without direct interaction with proprietary Thermo Fisher Scientific software.
• R Integration: Enables low-level infrastructure for proteomics data analysis within the R environment.
• In-Memory Data Handling: Maintains spectral objects in memory for rapid access and manipulation, with planned support for on-disc backend processing and lazy evaluation.

Scientific Applications:

• Proteomics Data Analysis: Supports exploration of raw MS data, extraction of intensity information for quantitative proteomics, and development of custom analysis pipelines in R.

Methodology:

rawR interfaces with Thermo Fisher Scientific raw files by wrapping the vendor-provided RawFileReader .NET assembly, enabling programmatic access to spectral and chromatographic data in a platform-independent R environment.