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DEIMoS GUI: An Open-Source User Interface for a High-Dimensional Mass Spectrometry Data Processing Tool

Journal Article · · Journal of Chemical Information and Modeling
 [1];  [1];  [1]
  1. Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
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In this paper, we report the creation of a graphical user interface (GUI) for the Data Extraction for Integrated Multidimensional Spectrometry (DEIMoS) tool. DEIMoS is a Python package to process data from high-dimensional mass spectrometry measurements. It is divided into several modules, each representing a data processing step, such as peak detection, alignment, and tandem mass spectra extraction and deconvolution. The inputs for and outputs from DEIMoS can include millions of N-dimensional data points, which can be challenging to visualize in a way that is interactive, informative, and responsive. Here, we used the HoloViz Python data stack, including DataShader and Param, to create an interactive visualization of mass spectrometry data. We believe the GUI will increase the accessibility of DEIMoS, and the visualization methods could be useful for other open-source mass spectrometry tools.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE Laboratory Directed Research and Development (LDRD) Program; National Institutes of Health (NIH)
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
2406933
Report Number(s):
PNNL-SA--187153
Journal Information:
Journal of Chemical Information and Modeling, Journal Name: Journal of Chemical Information and Modeling Journal Issue: 5 Vol. 64; ISSN 1549-9596
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English

References (8)

A practical guide to interpreting and generating bottom‐up proteomics data visualizations journal February 2022
AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization journal January 2021
DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data journal April 2022
A cross-platform toolkit for mass spectrometry and proteomics journal October 2012
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis journal May 2015
OpenMS: a flexible open-source software platform for mass spectrometry data analysis journal August 2016
Integrative analysis of multimodal mass spectrometry data in MZmine 3 journal March 2023
Matplotlib: A 2D Graphics Environment journal January 2007

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Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Aggregation
Calibration
DataShader
Deconvolution
Holoviz
Isotopes
Mass Spectrometry
Param