The rawrr R Package: Direct Access to Orbitrap Data and Beyond
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Date
2021-04-02
Publication Type
Journal Article
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yes
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Abstract
The Bioconductor project (Nat. Methods2015, 12 (2), 115–121) has shown that the R statistical environment is a highly valuable tool for genomics data analysis, but with respect to proteomics, we are still missing low-level infrastructure to enable performant and robust analysis workflows in R. Fundamentally important are libraries that provide raw data access. Our R package rawDiag (J. Proteome Res.2018, 17 (8), 2908–2914) has provided the proof-of-principle how access to mass spectrometry raw files can be realized by wrapping a vendor-provided advanced programming interface (API) for the purpose of metadata analysis and visualization. Our novel package rawrr now provides complete, OS-independent access to all spectral data logged in Thermo Fisher Scientific raw files. In this technical note, we present implementation details and describe the main functionalities provided by the rawrr package. In addition, we report two use cases inspired by real-world research tasks that demonstrate the application of the package. The raw data used for demonstration purposes was deposited as MassIVE data set MSV000086542. Availability: https://github.com/fgcz/rawrr.
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Publication status
published
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Book title
Journal / series
Volume
20 (4)
Pages / Article No.
2028 - 2034
Publisher
American Chemical Society
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Edition / version
Methods
Software
Geographic location
Date collected
Date created
Subject
computational mass spectrometry; software; R package
Organisational unit
02207 - Functional Genomics Center Zurich / Functional Genomics Center Zurich