Document Detail


MolFind: a software package enabling HPLC/MS-based identification of unknown chemical structures.
MedLine Citation:
PMID:  23039714     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
In this paper, we present MolFind, a highly multithreaded pipeline type software package for use as an aid in identifying chemical structures in complex biofluids and mixtures. MolFind is specifically designed for high-performance liquid chromatography/mass spectrometry (HPLC/MS) data inputs typical of metabolomics studies where structure identification is the ultimate goal. MolFind enables compound identification by matching HPLC/MS-based experimental data obtained for an unknown compound with computationally derived HPLC/MS values for candidate compounds downloaded from chemical databases such as PubChem. The downloaded "bins" consist of all compounds matching the monoisotopic molecular weight of the unknown. The computational HPLC/MS values predicted include retention index (RI), ECOM(50) (energy required to fragment 50% of a selected precursor ion), drift time, and collision induced dissociation (CID) spectrum. RI, ECOM(50), and drift-time models are used for filtering compounds downloaded from PubChem. The remaining candidates are then ranked based on CID spectra matching. Current RI and ECOM(50) models allow for the removal of about 28% of compounds from PubChem bins. Our estimates suggest that this could be improved to as much as 87% with additional chemical structures included in the computational models. Quantitative structure property relationship-based modeling of drift times showed a better correlation with experimentally determined drift times than did Mobcal cross-sectional areas. In 23 of 35 example cases, filtering PubChem bins with RI and ECOM(50) predictive models resulted in improved ranking of the unknown compounds compared to previous studies using CID spectra matching alone. In 19 of 35 examples, the correct candidate was ranked within the top 20 compounds in bins containing an average of 1635 compounds.
Authors:
Lochana C Menikarachchi; Shannon Cawley; Dennis W Hill; L Mark Hall; Lowell Hall; Steven Lai; Janine Wilder; David F Grant
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2012-10-23
Journal Detail:
Title:  Analytical chemistry     Volume:  84     ISSN:  1520-6882     ISO Abbreviation:  Anal. Chem.     Publication Date:  2012 Nov 
Date Detail:
Created Date:  2012-11-06     Completed Date:  2013-11-26     Revised Date:  2013-12-04    
Medline Journal Info:
Nlm Unique ID:  0370536     Medline TA:  Anal Chem     Country:  United States    
Other Details:
Languages:  eng     Pagination:  9388-94     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Chromatography, High Pressure Liquid / methods*
Mass Spectrometry / methods*
Software*
Grant Support
ID/Acronym/Agency:
1R01GM087714/GM/NIGMS NIH HHS; R01 GM087714/GM/NIGMS NIH HHS
Comments/Corrections

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