PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association
Abstract
Abstract Motivation Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. Results We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. Availability and implementation PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library. Supplementary information Supplementary data are available at Bioinformatics online.
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1430368
- Grant/Contract Number:
- AC05-76RLO 1830
- Resource Type:
- Published Article
- Journal Name:
- Bioinformatics
- Additional Journal Information:
- Journal Name: Bioinformatics Journal Volume: 33 Journal Issue: 17; Journal ID: ISSN 1367-4803
- Publisher:
- Oxford University Press
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Ma, Jian, Casey, Cameron P., Zheng, Xueyun, Ibrahim, Yehia M., Wilkins, Christopher S., Renslow, Ryan S., Thomas, Dennis G., Payne, Samuel H., Monroe, Matthew E., Smith, Richard D., Teeguarden, Justin G., Baker, Erin S., Metz, Thomas O., and Wren, ed., Jonathan. PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. United Kingdom: N. p., 2017.
Web. doi:10.1093/bioinformatics/btx305.
Ma, Jian, Casey, Cameron P., Zheng, Xueyun, Ibrahim, Yehia M., Wilkins, Christopher S., Renslow, Ryan S., Thomas, Dennis G., Payne, Samuel H., Monroe, Matthew E., Smith, Richard D., Teeguarden, Justin G., Baker, Erin S., Metz, Thomas O., & Wren, ed., Jonathan. PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. United Kingdom. https://doi.org/10.1093/bioinformatics/btx305
Ma, Jian, Casey, Cameron P., Zheng, Xueyun, Ibrahim, Yehia M., Wilkins, Christopher S., Renslow, Ryan S., Thomas, Dennis G., Payne, Samuel H., Monroe, Matthew E., Smith, Richard D., Teeguarden, Justin G., Baker, Erin S., Metz, Thomas O., and Wren, ed., Jonathan. Mon .
"PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association". United Kingdom. https://doi.org/10.1093/bioinformatics/btx305.
@article{osti_1430368,
title = {PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association},
author = {Ma, Jian and Casey, Cameron P. and Zheng, Xueyun and Ibrahim, Yehia M. and Wilkins, Christopher S. and Renslow, Ryan S. and Thomas, Dennis G. and Payne, Samuel H. and Monroe, Matthew E. and Smith, Richard D. and Teeguarden, Justin G. and Baker, Erin S. and Metz, Thomas O. and Wren, ed., Jonathan},
abstractNote = {Abstract Motivation Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. Results We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. Availability and implementation PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library. Supplementary information Supplementary data are available at Bioinformatics online.},
doi = {10.1093/bioinformatics/btx305},
journal = {Bioinformatics},
number = 17,
volume = 33,
place = {United Kingdom},
year = {Mon May 15 00:00:00 EDT 2017},
month = {Mon May 15 00:00:00 EDT 2017}
}
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