PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

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

doi:10.1093/bioinformatics/btx305

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

Journal Article · Mon May 15 00:00:00 EDT 2017 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btx305· OSTI ID:1430368

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

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.

View Journal Article

Sponsoring Organization:: USDOE

OSTI ID:: 1430368

Alternate ID(s):: OSTI ID: 1390434

Journal Information:: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 17 Vol. 33; ISSN 1367-4803

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (31)

Transport Properties of Ions in Gases Mason, Edward A.; McDaniel, Earl W. John Wiley & Sons, Inc. https://doi.org/10.1002/3527602852	book	January 1988
MetFusion: integration of compound identification strategies: MetFusion Gerlich, Michael; Neumann, Steffen Journal of Mass Spectrometry, Vol. 48, Issue 3 https://doi.org/10.1002/jms.3123	journal	February 2013
Ion mobility spectrometry-mass spectrometry (IMS-MS) of small molecules: Separating and assigning structures to ions Lapthorn, Cris; Pullen, Frank; Chowdhry, Babur Z. Mass Spectrometry Reviews, Vol. 32, Issue 1 https://doi.org/10.1002/mas.21349	journal	August 2012
Electrospray ionization with ambient pressure ion mobility separation and mass analysis by orthogonal time-of-flight mass spectrometry Steiner, Wes E.; Clowers, Brian H.; Fuhrer, Katrin Rapid Communications in Mass Spectrometry, Vol. 15, Issue 23 https://doi.org/10.1002/rcm.495	journal	January 2001
Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI) Sumner, Lloyd W.; Amberg, Alexander; Barrett, Dave Metabolomics, Vol. 3, Issue 3 https://doi.org/10.1007/s11306-007-0082-2	journal	September 2007
High-performance metabolic profiling with dual chromatography-Fourier-transform mass spectrometry (DC-FTMS) for study of the exposome Soltow, Quinlyn A.; Strobel, Frederick H.; Mansfield, Keith G. Metabolomics, Vol. 9, Issue S1 https://doi.org/10.1007/s11306-011-0332-1	journal	July 2011
Multiple sclerosis: Urinary amine measurement for orthomolecular diagnosis Robinson, Arthur B.; Westall, Fred C.; Ellison, George W. Life Sciences, Vol. 14, Issue 9 https://doi.org/10.1016/0024-3205(74)90276-8	journal	May 1974
Efficient tests for normality, homoscedasticity and serial independence of regression residuals Bera, Anil K.; Jarque, Carlos M. Economics Letters, Vol. 7, Issue 4 https://doi.org/10.1016/0165-1765(81)90035-5	journal	January 1981
An apparatus for the quantitative analysis of volatile compounds in urine Robinson, Arthur B.; Partridge, David; Turner, Martin Journal of Chromatography A, Vol. 85, Issue 1 https://doi.org/10.1016/S0021-9673(01)91860-6	journal	January 1973
An efficient data format for mass spectrometry-based proteomics Shah, Anuj R.; Davidson, Jennifer; Monroe, Matthew E. Journal of the American Society for Mass Spectrometry, Vol. 21, Issue 10 https://doi.org/10.1016/j.jasms.2010.06.014	journal	October 2010
The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results Ghavidel, Fatemeh Zamanzad; Mertens, Inge; Baggerman, Geert Journal of Proteomics, Vol. 98 https://doi.org/10.1016/j.jprot.2013.12.013	journal	February 2014
Measuring the Resolving Power of Ion Mobility Spectrometers Siems, William F.; Wu, Ching.; Tarver, Edward E. Analytical Chemistry, Vol. 66, Issue 23, p. 4195-4201 https://doi.org/10.1021/ac00095a014	journal	December 1994
XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification Smith, Colin A.; Want, Elizabeth J.; O'Maille, Grace Analytical Chemistry, Vol. 78, Issue 3 https://doi.org/10.1021/ac051437y	journal	February 2006
Targeted Profiling: Quantitative Analysis of ¹ H NMR Metabolomics Data Weljie, Aalim M.; Newton, Jack; Mercier, Pascal Analytical Chemistry, Vol. 78, Issue 13 https://doi.org/10.1021/ac060209g	journal	July 2006
Combined Ion Mobility/Time-of-Flight Mass Spectrometry Study of Electrospray-Generated Ions Guevremont, Roger; Siu, K. W. Michael; Wang, Jianyao Analytical Chemistry, Vol. 69, Issue 19 https://doi.org/10.1021/ac970359e	journal	October 1997
CIUSuite: A Quantitative Analysis Package for Collision Induced Unfolding Measurements of Gas-Phase Protein Ions Eschweiler, Joseph D.; Rabuck-Gibbons, Jessica N.; Tian, Yuwei Analytical Chemistry, Vol. 87, Issue 22 https://doi.org/10.1021/acs.analchem.5b03292	journal	October 2015
Quantifying the stabilizing effects of protein–ligand interactions in the gas phase Allison, Timothy M.; Reading, Eamonn; Liko, Idlir Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9551	journal	October 2015
LipidBlast in silico tandem mass spectrometry database for lipid identification Kind, Tobias; Liu, Kwang-Hyeon; Lee, Do Yup Nature Methods, Vol. 10, Issue 8 https://doi.org/10.1038/nmeth.2551	journal	June 2013
Quantitative Analysis of Urine Vapor and Breath by Gas-Liquid Partition Chromatography Pauling, L.; Robinson, A. B.; Teranishi, R. Proceedings of the National Academy of Sciences, Vol. 68, Issue 10 https://doi.org/10.1073/pnas.68.10.2374	journal	October 1971
'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data Nicholson, J. K.; Lindon, J. C.; Holmes, E. Xenobiotica, Vol. 29, Issue 11 https://doi.org/10.1080/004982599238047	journal	January 1999
Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results Castle, A. L. Briefings in Bioinformatics, Vol. 7, Issue 2 https://doi.org/10.1093/bib/bbl008	journal	March 2006
DAnTE: a statistical tool for quantitative analysis of -omics data Polpitiya, A. D.; Qian, W. -J.; Jaitly, N. Bioinformatics, Vol. 24, Issue 13 https://doi.org/10.1093/bioinformatics/btn217	journal	May 2008
LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets Crowell, Kevin L.; Slysz, Gordon W.; Baker, Erin S. Bioinformatics, Vol. 29, Issue 21 https://doi.org/10.1093/bioinformatics/btt465	journal	September 2013
MetaboAnalyst 3.0—making metabolomics more meaningful Xia, Jianguo; Sinelnikov, Igor V.; Han, Beomsoo Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv380	journal	April 2015
Multiple Object Tracking Using K-Shortest Paths Optimization Berclaz, J.; Fleuret, F.; Turetken, E. IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 33, Issue 9 https://doi.org/10.1109/TPAMI.2011.21	journal	September 2011
Iteratively Reweighted Least Squares: Algorithms, Convergence Analysis, and Numerical Comparisons Wolke, R.; Schwetlick, H. SIAM Journal on Scientific and Statistical Computing, Vol. 9, Issue 5 https://doi.org/10.1137/0909062	journal	September 1988
A Method for the Solution of the Nth Best Path Problem Hoffman, Walter; Pavley, Richard Journal of the ACM, Vol. 6, Issue 4 https://doi.org/10.1145/320998.321004	journal	October 1959
Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data Jaitly, Navdeep; Mayampurath, Anoop; Littlefield, Kyle BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-87	journal	January 2009
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data Pluskal, Tomáš; Castillo, Sandra; Villar-Briones, Alejandro BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-395	journal	July 2010
MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis LaMarche, Brian L.; Crowell, Kevin L.; Jaitly, Navdeep BMC Bioinformatics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2105-14-49	journal	January 2013
Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go? Metz, Thomas O.; Baker, Erin S.; Schymanski, Emma L. Bioanalysis, Vol. 9, Issue 1 https://doi.org/10.4155/bio-2016-0244	journal	January 2017

Similar Records

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

Journal Article · Mon May 15 00:00:00 EDT 2017 · Bioinformatics · OSTI ID:1390434

AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry

Journal Article · Fri Jun 18 20:00:00 EDT 2021 · Bioinformatics · OSTI ID:1888830

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

Citation Formats

References (31)

Similar Records

Related Subjects