U.S. Department of Energy

Pacific Northwest National Laboratory

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.

TitleLC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.
Publication TypeJournal Article
Year of Publication2013
AuthorsCrowell KL, Slysz GW, Baker ES, LaMarche BL, Monroe ME, Ibrahim YM, Payne SH, Anderson GA, Smith RD
JournalBioinformatics
Abstract

MOTIVATION: The addition of ion mobility spectrometry to liquid chromatography-mass spectrometry experiments requires new, or updated, software tools to facilitate data processing.

RESULTS: We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension.

AVAILABILITY: LC-IMS-MS Feature Finder is available as a command-line tool for download at http://omics.pnl.gov/software/lc-ims-ms-feature-finder. The Microsoft.NET Framework 4.0 is required to run the software. All other dependencies are included with the software package. Usage of this software is limited to non-profit research to use (see README).

CONTACT: rds@pnnl.gov.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI10.1093/bioinformatics/btt465
PubMed ID24008421
PubMed Central IDPMC3799467
Grant List8 P41 GM103493-10 / GM / NIGMS NIH HHS / United States
R01ES022190 / ES / NIEHS NIH HHS / United States
Area of Research: 
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