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Updated: May 24, 2025

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models
Published on: December 5, 2014
arcMS: transformation of multi-dimensional high-resolution mass spectrometry data to columnar format for compact
1LEESU, Univ Paris Est Créteil, Ecole des des Ponts, Créteil F-94010, France.
Summary:
The arcMS R package addresses the challenges posed by proprietary and open-source high-resolution mass spectrometry data formats by providing functions to collect MSE data from the Waters UNIFI software and store it in the efficient Apache Parquet format, facilitating fast, easy access, and compatibility with various programming environments. This solution facilitates the manipulation of complex mass spectrometry data, including ion mobility or other additional dimensions, enabling potential integration into efficient and open-source workflows.
Availability And Implementation:
arcMS is an open-source R package and is available on GitHub at https://github.com/leesulab/arcMS. The complete documentation, including details on UNIFI configuration and tutorials for data conversion, access to Parquet files, and filtration of data, is available at https://leesulab.github.io/arcMS. An R/Shiny companion application is also provided for visualization of Parquet data and demonstration of data filtering with the Arrow library https://github.com/leesulab/arcms-dataviz.
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