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:1390434

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.

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 by 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.

• Research Organization: Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1390434
• Report Number(s): PNNL-SA-122828; 49183; 48246
• Journal Information: Bioinformatics, Vol. 33, Issue 17; ISSN 1367-4803
• Publisher: Oxford University Press
• Country of Publication: United States
• Language: English

Related Subjects

Environmental Molecular Sciences Laboratory