DEIMoS, or Data Extraction for Integrated Multidimensional Spectrometry, is a Python application programming interface and command-line tool for high-dimensional mass spectrometry (MS) data analysis workflows that offers ease of development and access to efficient algorithmic implementations. Functionality includes feature detection, feature alignment, collision cross section (CCS) calibration, isotope detection, and MS/MS spectral deconvolution, with the output comprising detected features aligned across study samples and characterized by mass, CCS, tandem mass spectra, and isotopic signature. Notably, DEIMoS operates on N-dimensional data, largely agnostic to acquisition instrumentation; algorithm implementations simultaneously utilize all dimensions to (i) offer greater separation between features, thus improving detection sensitivity, (ii) increase alignment/feature matching confidence among datasets, and (iii) mitigate convolution artifacts in tandem mass spectra.
.. toctree::
:caption: Getting Started
:name: getting_started
:hidden:
:maxdepth: 1
getting_started/installation
getting_started/example_data
getting_started/cli
.. toctree::
:caption: User Guide
:name: user_guide
:hidden:
:maxdepth: 1
user_guide/loading_saving
user_guide/peak_detection
user_guide/ccs_calibration
user_guide/ms2_extraction
user_guide/isotope_detection
user_guide/extracted_ion
user_guide/alignment
.. toctree::
:caption: API Reference
:name: api_reference
:hidden:
:maxdepth: 1
api_reference/deimos
api_reference/alignment
api_reference/calibration
api_reference/cli
api_reference/deconvolution
api_reference/filters
api_reference/grid
api_reference/io
api_reference/isotopes
api_reference/peakpick
api_reference/plot
api_reference/subset
api_reference/utils
.. toctree::
:caption: Project Info
:name: project_info
:hidden:
:maxdepth: 1
project_info/acknowledgements
project_info/citing_and_citations
project_info/contributing
project_info/license
project_info/disclaimer