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

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [1];  [1]
  1. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
  2. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 93771, USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1430368
Grant/Contract Number:
AC05-76RLO 1830
Resource Type:
Journal Article: Published Article
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Volume: 33; Journal Issue: 17; Related Information: CHORUS Timestamp: 2018-03-28 22:40:34; 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., and Metz, Thomas O.. 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.. PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. United Kingdom. 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., and Metz, Thomas O.. Mon . "PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association". United Kingdom. doi: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.},
abstractNote = {},
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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1093/bioinformatics/btx305

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  • Motivation: Drift tube ion mobility spectrometry (DTIMS) 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 coupled with mass spectrometry 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 information necessary to create a reference library containing accu-rate masses, DTIMS arrival times and CCSs for use in high throughput omics analyses. Results: We demonstrate the utility of this approach bymore » automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were identical to those calculated by hand and within error of those calcu-lated using commercially available instrument vendor software.« less
  • DTIMS collision cross section database for metabolites and xenobiotics.
  • Collision cross section (CCS) measurements resulting from ion mobility-mass spectrometry (IM-MS) experiments provide a promising orthogonal dimension of structural information in MS-based analytical separations. As with any molecular identifier, interlaboratory standardization must precede broad range integration into analytical workflows. In this study, we present a reference drift tube ion mobility mass spectrometer (DTIM-MS) where improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (DTCCSN2) for over 120 unique ion species with the lowest measurement uncertainty to date. The reproducibility of these DTCCSN2 values are evaluated across three additional laboratories on amore » commercially available DTIM-MS instrument. The traditional stepped field CCS method performs with a relative standard deviation (RSD) of 0.29% for all ion species across the three additional laboratories. The calibrated single field CCS method, which is compatible with a wide range of chromatographic inlet systems, performs with an average, absolute bias of 0.54% to the standardized stepped field DTCCSN2 values on the reference system. The low RSD and biases observed in this interlaboratory study illustrate the potential of DTIM-MS for providing a molecular identifier for a broad range of discovery based analyses.« less
  • First, simulated chromatographic separations with declining retention time precision were used to study the performance of the piecewise retention time alignment algorithm and to demonstrate an unsupervised parameter optimization method. The average correlation coefficient between the first chromatogram and every other chromatogram in the data set was used to optimize the alignment parameters. This correlation method does not require a training set, so it is unsupervised and automated. This frees the user from needing to provide class information and makes the alignment algorithm more generally applicable to classifying completely unknown data sets. For a data set of simulated chromatograms wheremore » the average chromatographic peak was shifted past two neighboring peaks between runs, the average correlation coefficient of the raw data was 0.46 ± 0.25. After automated, optimized piecewise alignment, the average correlation coefficient was 0.93 ± 0.02. Additionally, a relative shift metric and principal component analysis (PCA) were used to independently quantify and categorize the alignment performance, respectively. The relative shift metric was defined as four times the standard deviation of a given peak’s retention time in all of the chromatograms, divided by the peak-width-at-base. The raw simulated data sets that were studied contained peaks with average relative shifts ranging between 0.3 and 3.0. Second, a “real” data set of gasoline separations was gathered using three different GC methods to induce severe retention time shifting. In these gasoline separations, retention time precision improved ~8 fold following alignment. Finally, piecewise alignment and the unsupervised correlation optimization method were applied to severely shifted GC separations of reformate distillation fractions. The effect of piecewise alignment on peak heights and peak areas is also reported. Piecewise alignment either did not change the peak height, or caused it to slightly decrease. The average relative difference in peak height after piecewise alignment was –0.20%. Piecewise alignment caused the peak areas to either stay the same, slightly increase, or slightly decrease. The average absolute relative difference in area after piecewise alignment was 0.15%.« less
  • Time of flight secondary ion mass spectrometry (ToF SIMS) is one of the most powerful characterization tools allowing imaging of the chemical properties of various systems and materials. It allows precise studies of the chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF SIMS results is challengeable, because of the data volume and its multidimensionality. Furthermore, investigation of the samples with pronounced topographical features are complicated by the spectral shift. In this work we developed approach for the comprehensive ToF SIMS data interpretation based on the data analytics and automated extraction of the samplemore » topography based on time of flight shift. We further applied this approach to investigate correlation between biological function and chemical composition in Arabidopsis roots.« less