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Title: Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra

Abstract

Ultrahigh-resolution mass spectrometry, such as Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work we describe a user friendly interface for CIA, titled Formularity, which includes an additional functionality to perform search of formulas based on an Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. The HOC spike in NOM and tap water were used to assess HOC identification in natural and anthropogenic matrices. Strategies for reconciliation of CIA and IPA assignments are discussed. Software and sample databases with documentation are freely available from the PNNL OMICS software repository https://omics.pnl.gov/software/formularity.

Authors:
ORCiD logo [1]; ORCiD logo [1];  [1];  [1];  [1];  [2];  [2]; ORCiD logo [3];  [1];  [1];  [1]
  1. Earth &, Biological Sciences Division, Pacific Northwest National Laboratory (PNNL), Richland, Washington 99354, United States
  2. Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution (WHOI), Woods Hole, Massachusetts 02543, United States
  3. Marine Sciences Laboratory (MSL), Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1422342
Report Number(s):
PNNL-SA-128094
Journal ID: ISSN 0003-2700; 49222; KP1704020
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Analytical Chemistry; Journal Volume: 89; Journal Issue: 23
Country of Publication:
United States
Language:
English
Subject:
data analysis; formula assignment; Fourier transform ion cyclotron resonance; natural organic matter; software; halogenated organic compounds; Environmental Molecular Sciences Laboratory

Citation Formats

Tolić, Nikola, Liu, Yina, Liyu, Andrey, Shen, Yufeng, Tfaily, Malak M., Kujawinski, Elizabeth B., Longnecker, Krista, Kuo, Li-Jung, Robinson, Errol W., Paša-Tolić, Ljiljana, and Hess, Nancy J. Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra. United States: N. p., 2017. Web. doi:10.1021/acs.analchem.7b03318.
Tolić, Nikola, Liu, Yina, Liyu, Andrey, Shen, Yufeng, Tfaily, Malak M., Kujawinski, Elizabeth B., Longnecker, Krista, Kuo, Li-Jung, Robinson, Errol W., Paša-Tolić, Ljiljana, & Hess, Nancy J. Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra. United States. doi:10.1021/acs.analchem.7b03318.
Tolić, Nikola, Liu, Yina, Liyu, Andrey, Shen, Yufeng, Tfaily, Malak M., Kujawinski, Elizabeth B., Longnecker, Krista, Kuo, Li-Jung, Robinson, Errol W., Paša-Tolić, Ljiljana, and Hess, Nancy J. Mon . "Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra". United States. doi:10.1021/acs.analchem.7b03318.
@article{osti_1422342,
title = {Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra},
author = {Tolić, Nikola and Liu, Yina and Liyu, Andrey and Shen, Yufeng and Tfaily, Malak M. and Kujawinski, Elizabeth B. and Longnecker, Krista and Kuo, Li-Jung and Robinson, Errol W. and Paša-Tolić, Ljiljana and Hess, Nancy J.},
abstractNote = {Ultrahigh-resolution mass spectrometry, such as Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work we describe a user friendly interface for CIA, titled Formularity, which includes an additional functionality to perform search of formulas based on an Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. The HOC spike in NOM and tap water were used to assess HOC identification in natural and anthropogenic matrices. Strategies for reconciliation of CIA and IPA assignments are discussed. Software and sample databases with documentation are freely available from the PNNL OMICS software repository https://omics.pnl.gov/software/formularity.},
doi = {10.1021/acs.analchem.7b03318},
journal = {Analytical Chemistry},
number = 23,
volume = 89,
place = {United States},
year = {Mon Nov 13 00:00:00 EST 2017},
month = {Mon Nov 13 00:00:00 EST 2017}
}