Overview
arcMS converts Waters UNIFI MS-E and HDMS-E data into tabular Parquet or HDF5 storage for analysis in R or Python. It also documents mzML-to-Parquet conversion, metadata retrieval and access to mobility/CCS information when available.
What can this tool do?
Common uses
- arcMS converts Waters UNIFI MS-E and HDMS-E data into tabular Parquet or HDF5 storage for analysis in R or Python.
Scientific fit
Primary function
Data conversion and import
Other functions
Data management and sharing
Data compatibility
Inputs
Raw instrument data, Mass spectra
Outputs
Mass spectra
Input formats
UNIFI API MS-E/HDMS-E data or supported mzML files
Output formats
Parquet plus JSON metadata, or HDF5 spectral/metadata datasets
Scope and considerations
Designed for
- arcMS converts Waters UNIFI MS-E and HDMS-E data into tabular Parquet or HDF5 storage for analysis in R or Python.
Not designed for
- Automatic feature detection, spectral deconvolution or molecular identification from the converted data.
Important requirements
- R and documented dependencies; UNIFI conversion requires configured API access and registered connection credentials, while HDF5 use requires its supporting packages.
Considerations
- Keep acquisition metadata with exported arrays and distinguish measured mobility/CCS fields from predicted values. The separate companion visualization app has its own setup.
Access and documentation
MIT source distribution. External datasets, dependent packages and any hosted routes retain their own terms; software operation was not tested.
License: MIT
Evidence and review
Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch3.md.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- arcMS: transformation of multi-dimensional high-resolution mass spectrometry data to columnar format for compact storage and fast access. Bioinformatics Advances (2024). doi:10.1093/bioadv/vbae160
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-27 · First committed entry
Add 45 source-reviewed Enveda tool entries in third expansion batch
View change · Entry at this revision