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

被引：0
|
作者：
Oostrom, Marjolein T. [1 ]
Colby, Sean M. [2 ]
Metz, Thomas O. [2 ]
机构：
[1] Pacific Northwest Natl Lab, Natl Secur Directorate, Richland, WA 99352 USA
[2] Pacific Northwest Natl Lab, Earth & Biol Sci Directorate, Richland, WA 99352 USA
来源：
JOURNAL OF CHEMICAL INFORMATION AND MODELING | 2024年 / 64卷 / 05期
基金：
美国国家卫生研究院;
关键词：
PLATFORM;
D O I：
10.1021/acs.jcim.3c01222
中图分类号：
R914 [药物化学];
学科分类号：
100701 ;
摘要：
We report here the creation of a graphical user interface (GUI) for the Data Extraction for Integrated Multidimensional Spectrometry (DEIMoS) tool. DEIMoS is a Python package that processes 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 visualization stack, including DataShader and Param, to create an interactive visualization of the mass spectrometry data. We believe the GUI will increase the accessibility of DEIMoS and that the visualization methods could be useful for other open-source mass spectrometry tools.
引用
收藏
页码：1419 / 1424
页数：6
相关论文
共 50 条
  • [31] Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data
    Caroline Truntzer
    Elise Mostacci
    Aline Jeannin
    Jean-Michel Petit
    Patrick Ducoroy
    Hervé Cardot
    BMC Bioinformatics, 15
  • [32] SPOT: Open source visual data analytics platform for high-dimensional scientific data
    Diblen, F.
    Attema, J. J.
    Bakhshi, R.
    Stienen, B.
    Hendriks, L.
    Caron, S.
    2018 IEEE 14TH INTERNATIONAL CONFERENCE ON E-SCIENCE (E-SCIENCE 2018), 2018, : 411 - 411
  • [33] Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data
    Truntzer, Caroline
    Mostacci, Elise
    Jeannin, Aline
    Petit, Jean-Michel
    Ducoroy, Patrick
    Cardot, Herve
    BMC BIOINFORMATICS, 2014, 15
  • [34] Constellation: An Open-Source Web Application for Unsupervised Systematic Trend Detection in High-Resolution Mass Spectrometry Data
    Letourneau, Dane R.
    Volmer, Dietrich A.
    JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 2022, 33 (02) : 382 - 389
  • [35] inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction
    Cormican, John A.
    Horokhovskyi, Yehor
    Soh, Wai Tuck
    Mishto, Michele
    Liepe, Juliane
    MOLECULAR & CELLULAR PROTEOMICS, 2022, 21 (12)
  • [36] MVP - an open-source preprocessor for cleaning duplicate records and missing values in mass spectrometry data
    Lee, Geunho
    Lee, Hyun Beom
    Jung, Byung Hwa
    Nam, Hojung
    FEBS OPEN BIO, 2017, 7 (07): : 1051 - 1059
  • [37] Constructing metabolic association networks using high-dimensional mass spectrometry data
    Koo, Imhoi
    Wei, Xiaoli
    Shi, Xue
    Zhou, Zhanxiang
    Kim, Seongho
    Zhang, Xiang
    CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 2014, 138 : 193 - 202
  • [38] MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data
    Naake, Thomas
    Rainer, Johannes
    Huber, Wolfgang
    BIOINFORMATICS, 2023, 39 (10)
  • [39] CrossCheck: an open-source web tool for high-throughput screen data analysis
    Najafov, Jamil
    Najafov, Ayaz
    SCIENTIFIC REPORTS, 2017, 7
  • [40] CrossCheck: an open-source web tool for high-throughput screen data analysis
    Jamil Najafov
    Ayaz Najafov
    Scientific Reports, 7
12345