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The rawrr R Package: Direct Access to Orbitrap Data and Beyond.

Tobias Kockmann1, Christian Panse1,2

  • 1Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

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The rawrr R package offers complete, OS-independent access to Thermo Fisher Scientific mass spectrometry raw files. This enables robust proteomics data analysis workflows in R, enhancing research capabilities.

Keywords:
R packagecomputational mass spectrometrysoftware

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Area of Science:

  • Proteomics
  • Computational Biology
  • Bioinformatics

Background:

  • The R statistical environment is crucial for genomics but lacks robust infrastructure for proteomics analysis.
  • Access to raw mass spectrometry data is fundamental for developing advanced proteomics workflows.
  • Previous R packages like rawDiag demonstrated proof-of-principle for raw file access but were limited.

Purpose of the Study:

  • To introduce the rawrr R package for comprehensive access to Thermo Fisher Scientific raw files.
  • To provide OS-independent access to all spectral data within mass spectrometry raw files.
  • To demonstrate the utility of rawrr through real-world research use cases.

Main Methods:

  • Development of the rawrr R package, leveraging vendor-provided advanced programming interfaces (APIs).
  • Implementation of OS-independent data access for Thermo Fisher Scientific raw files.
  • Demonstration of package functionalities using two distinct research-inspired use cases.

Main Results:

  • The rawrr package provides complete, OS-independent access to spectral data in Thermo Fisher Scientific raw files.
  • The package facilitates metadata analysis, visualization, and direct spectral data extraction.
  • Use cases illustrate efficient application for proteomics data analysis tasks.

Conclusions:

  • The rawrr package significantly enhances R's capabilities for proteomics data analysis.
  • It addresses the need for low-level infrastructure for performant and robust proteomics workflows in R.
  • rawrr empowers researchers with direct access to raw mass spectrometry data, facilitating deeper insights.