IROA Publications
IROA Publications

Advancing Science.
Enabling Discovery.

Explore peer-reviewed research publications that highlight the power of accurate measurement and innovative analytical solutions.

100+

Publications

5,200+

Citations

250+

Researchers

20+

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High-Impact Journals
01
Research Article

Achieving Effective Batch-to-Batch Error Correction through Suppression Correction and Dual MSTUS Normalization

Debasish Ghosh, Janmejoy Kar, Felice A de Jong, Chris Beecher, Vladimir Shulaev
Analytical Chemistry 98(15)
April 1, 2026
https://doi.org/10.1021/acs.analchem.5c05210
Open Access
Abstract

Batch effect corrections are necessary to remove instrumentally introduced variance but should retain biological variance. Most common batch correction techniques are based on analysis of quality control (QC) samples, sample amplitude normalization, or other statistical and normalization techniques. Many of these approaches correct for the totality of the MS signal and do not differentiate between analytical and biological variances. In this study, Saccharomyces cerevisiae was treated with four different oxidants at five different time points. Biologically replicated sample sets were…

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02
Book Chapter

Isotopic Ratio Outlier Analysis (IROA) for Quantitative Analysis

Chris Beecher, Felice A de Jong
Methods in molecular biology (Clifton, N.J.) 2925:69-89
June 1, 2025
https://doi.org/10.1007/978-1-0716-4534-5_4
Abstract

Metabolomics is an omics science that tries to measure the metabolic composition of a sample rapidly, but the current state of the art cannot provide the reproducibility or accuracy needed for clinical use or even daily reproducibility for larger experiments. The IROA TruQuant Workflow uses a daily long-term reference standard (LTRS) and a chemically identical Internal Standard (IS) to provide validated chemical identity, accurate reproducible quantitation, and daily QA/QC (Quality Assurance / Quality Control) on instrument and sample preparation. It…

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03
Research Article

Ion suppression correction and normalization for non-targeted metabolomics

Iqbal Mahmud, Bo Wei, Lucas Veillon, Lin Tan, Sara Martinez, Bao Tran, Alexander Raskind, Felice A de Jong, Yiwei (Eve) Liu, Jibin Ding
Nature Communications
February 1, 2025
https://doi.org/10.1038/s41467-025-56646-8
Open Access
Abstract

Ion suppression is a major problem in mass spectrometry (MS)-based metabolomics; it can dramatically decrease measurement accuracy, precision, and sensitivity. Here we report a method, the IROA TruQuant Workflow, that uses a stable isotope-labeled internal standard (IROA-IS) library plus companion algorithms to: 1) measure and correct for ion suppression, and 2) perform Dual MSTUS normalization of MS metabolomic data. We evaluate the method across ion chromatography (IC), hydrophilic interaction liquid chromatography (HILIC), and reversed-phase liquid chromatography (RPLC)-MS systems in both…

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04
Research Article

An IROA Workflow for correction and normalization of ion suppression in mass spectrometry-based metabolomic profiling data

Iqbal Mahmud, Bo Wei, Lucas Veillon, Lin Tan, Sara Martinez, Bao Tran, Alexander Raskind, Rehan Akbani, John N Weinstein, Chris Beecher
February 1, 2024
https://doi.org/10.21203/rs.3.rs-3914827/v1
Abstract

Ion suppression is a major problem in mass spectrometry (MS)-based metabolomics; it can dramatically decrease measurement accuracy, precision, and signal-to-noise sensitivity. Here we report a new method, the IROA TruQuant Workflow, that uses a stable isotope-labeled internal standard (IROA-IS) plus novel companion algorithms to 1) measure and correct for ion suppression, and 2) perform Dual MSTUS normalization of MS metabolomic data. We have evaluated the method across ion chromatography (IC), hydrophilic interaction liquid chromatography (HILIC), and reverse phase liquid chromatography…

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05
Research Article

Establishing a framework for best practices for quality assurance and quality control in untargeted metabolomics

Jonathan D Mosley, Tracey B Schock, Chris Beecher, Warwick B Dunn, Julia Kuligowski, Matthew R. Lewis, Georgios Theodoridis, Candice Zena Ulmer Holland, Vuckovic Dajana, Ian D Wilson, Krista A Zanetti
Metabolomics 20(2)
February 1, 2024
https://doi.org/10.1007/s11306-023-02080-0
Open Access
Abstract

Background Quality assurance (QA) and quality control (QC) practices are key tenets that facilitate study and data quality across all applications of untargeted metabolomics. These important practices will strengthen this field and accelerate its success. The Best Practices Working Group (WG) within the Metabolomics Quality Assurance and Quality Control Consortium (mQACC) focuses on community use of QA/QC practices and protocols and aims to identify, catalogue, harmonize, and disseminate current best practices in untargeted metabolomics through community-driven activities. Aim of review…

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06
Research Article

Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC)

Katrice A. Lippa, Juan J. Aristizabal-Henao, Richard D Beger, John A. Bowden, Corey D Broeckling, Chris Beecher, W. Clay Davis, Warwick B Dunn, Roberto Flores, Royston Goodacre
Metabolomics 18(4)
April 1, 2022
https://doi.org/10.1007/s11306-021-01848-6
Open Access
Abstract

Introduction The metabolomics quality assurance and quality control consortium (mQACC) is enabling the identification, development, prioritization, and promotion of suitable reference materials (RMs) to be used in quality assurance (QA) and quality control (QC) for untargeted metabolomics research. Objectives This review aims to highlight current RMs, and methodologies used within untargeted metabolomics and lipidomics communities to ensure standardization of results obtained from data analysis, interpretation and cross-study, and cross-laboratory comparisons. The essence of the aims is also applicable to other…

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07
Research Article

Dissemination and analysis of the quality assurance (QA) and quality control (QC) practices of LC–MS based untargeted metabolomics practitioners

Anne Marie Evans, Claire C O'Donovan, Mary Playdon, Chris Beecher, Richard D Beger, John A. Bowden, David Broadhurst, Clary Clish, Surendra Dasari, Warwick B Dunn, Tao Huan
Metabolomics 16(10)
October 1, 2020
https://doi.org/10.1007/s11306-020-01728-5
Open Access
Abstract

IntroductionThe metabolomics quality assurance and quality control consortium (mQACC) evolved from the recognized need for a community-wide consensus on improving and systematizing quality assurance (QA) and quality control (QC) practices for untargeted metabolomics.Objectives In this work, we sought to identify and share the common and divergent QA and QC practices amongst mQACC members and collaborators who use liquid chromatography-mass spectrometry (LC–MS) in untargeted metabolomics.Methods All authors voluntarily participated in this collaborative research project by providing the details of and insights…

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08
Research Article

Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment

Nicholas J Taylo, Irina Gaynanova, Steven A Eschrich, Eric A. Welsh, Timothy J Garrett, Chris Beecher, Ritin Sharma, John Koomen, Keiran Smalley, Jane L Messina, Peter A. Kanetsky
PLOS PLOS One
October 1, 2020
https://doi.org/10.1371/journal.pone.0240849
Open Access
Abstract

Background Melanoma causes the vast majority of deaths attributable to skin cancer, largely due to its propensity for metastasis. To date, few studies have examined molecular changes between primary cutaneous melanoma and adjacent putatively normal skin. To broaden temporal inferences related to initiation of disease, we performed a metabolomics investigation of primary melanoma and matched extratumoral microenvironment (EM) tissues; and, to make inferences about progressive disease, we also compared unmatched metastatic melanoma tissues to EM tissues. Methods Ultra-high performance liquid…

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09
Research Article

Integration of Standards for Ion Suppression Correction and QC in an Untargeted Metabolomics Workflow

White Paper, Chris Beecher, Felice A de Jong
January 1, 2020
https://doi.org/10.13140/RG.2.2.28112.74245
Open Access
Abstract

The lack of reproducible data due to matrix effects in untargeted metabolomics has been an on-going major concern. Ion suppression, interference from coeluted chemical components (sample matrix, solvent or LC-MS system components), is often observed as the loss of analyte ionization response and negatively affects precision, accuracy, and reproducibility (over- or underestimation of analyte levels). The optimization and validation of quantitative LC-MS methods relies on the assessment and correction of ion suppression. We conducted a simple experimental to understand the…

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10
Research Article

An Isotopic Ratio Outlier Analysis Approach for Global Metabolomics of Biosynthetically Talented Actinomycetes

Jordan Carey, Thanh Nguyen, Jennifer Korchak, Chris Beecher, Felice A de Jong, Amy Lane
September 1, 2019
https://doi.org/10.3390/metabo9090181
Open Access
Abstract

Actinomycetes are powerhouses of natural product biosynthesis. Full realization of this biosynthetic potential requires approaches for recognizing novel metabolites and determining mediators of metabolite production. Herein, we develop an isotopic ratio outlier analysis (IROA) ultra-high performance liquid chromatography-mass spectrometry (UHPLC/MS) global metabolomics strategy for actinomycetes that facilitates recognition of novel metabolites and evaluation of production mediators. We demonstrate this approach by determining impacts of the iron chelator 2,2′-bipyridyl on the Nocardiopsis dassonvillei metabolome. Experimental and control cultures produced metabolites with…

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Showing 1–10 of 121 publications