A statistical framework for protein quantitation in bottom-up MS-based proteomics. - Yuliya V. Karpievitch; Jeff Stanley; Thomas Taverner; Jianhua Huang; Joshua N. Adkins; Charles Ansong; Fred Heffron; Thomas O. Metz; Wei-Jun Qian; Hyunjin Yoon; Richard D. Smith; Alan R. Dabney (Bioinform., 2009)

Charge Prediction of Lipid Fragments in Mass Spectrometry. - Brian T. Schrom; Lars J. Kangas; Bojana Ginovska-Pangovska; Thomas O. Metz; John H. Miller (ICMLA (2), 2011)

Improved quality control processing of peptide-centric LC-MS proteomics data. - Melissa M. Matzke; Katrina M. Waters; Thomas O. Metz; Jon M. Jacobs; Amy C. Sims; Ralph S. Baric; Joel G. Pounds; Bobbie-Jo M. Webb-Robertson (Bioinform., 2011)

In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids. - Lars J. Kangas; Thomas O. Metz; Giorgis Isaac; Brian T. Schrom; Bojana Ginovska-Pangovska; Luning Wang; Li Tan; Robert R. Lewis; John H. Miller (Bioinform., 2012)

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. - Brian J. Schmidt; Ali Ebrahim; Thomas O. Metz; Joshua N. Adkins; Bernhard Ø. Palsson; Daniel R. Hyduke (Bioinform., 2013)

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. - Brian L. LaMarche; Kevin L. Crowell; Navdeep Jaitly; Vladislav A. Petyuk; Anuj R. Shah; Ashoka D. Polpitiya; John D. Sandoval; Gary R. Kiebel; Matthew E. Monroe; Stephen J. Callister; Thomas O. Metz; Gordon A. Anderson; et al. (BMC Bioinform., 2013)

Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. - Nicolas Tchitchek; Amie J. Eisfeld; Jennifer Tisoncik-Go; Laurence Josset; Lisa E. Gralinski; Christophe Bécavin; Susan C. Tilton; Bobbie-Jo M. Webb-Robertson; Martin T. Ferris; Allison L. Totura; Chengjun Li; Gabriele Neumann; et al. (BMC Syst. Biol., 2013)

Building a Molecular Glyco-phenotype Ontology to Decipher Undiagnosed Diseases. - Jean-Philippe F. Gourdine; Thomas O. Metz; David Koeller; Matthew H. Brush; Melissa A. Haendel (ICBO/BioCreative, 2016)

LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. - Jennifer E. Kyle; Kevin L. Crowell; Cameron P. Casey; Grant M. Fujimoto; Sangtae Kim; Sydney E. Dautel; Richard D. Smith; Samuel H. Payne; Thomas O. Metz (Bioinform., 2017)

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. - Jian Ma; Cameron P. Casey; Xueyun Zheng; Yehia M. Ibrahim; Christopher S. Wilkins; Ryan S. Renslow; Dennis G. Thomas; Samuel H. Payne; Matthew E. Monroe; Richard D. Smith; Justin G. Teeguarden; Erin S. Baker; et al. (Bioinform., 2017)

An automated framework for NMR chemical shift calculations of small organic molecules. - Yasemin Yesiltepe; Jamie R. Nuñez; Sean M. Colby; Dennis G. Thomas; Mark I. Borkum; Patrick Reardon; Nancy M. Washton; Thomas O. Metz; Justin G. Teeguarden; Niranjan Govind; Ryan S. Renslow (J. Cheminformatics, 2018)

Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples. - Jamie R. Nuñez; Sean M. Colby; Dennis G. Thomas; Malak M. Tfaily; Nikola Tolic; Elin M. Ulrich; Jon R. Sobus; Thomas O. Metz; Justin G. Teeguarden; Ryan S. Renslow (J. Chem. Inf. Model., 2019)

Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets. - Jamie R. Nuñez; Monee Y. McGrady; Yasemin Yesiltepe; Ryan S. Renslow; Thomas O. Metz (J. Chem. Inf. Model., 2020)

Similarity Downselection: A Python implementation of a heuristic search algorithm for finding the set of the n most dissimilar items with an application in conformer sampling. - Felicity F. Nielson; Sean M. Colby; Ryan S. Renslow; Thomas O. Metz (CoRR, 2021)

SPECTRe: Substructure Processing, Enumeration, and Comparison Tool Resource: An efficient tool to encode all substructures of molecules represented in SMILES. - Yasemin Yesiltepe; Ryan S. Renslow; Thomas O. Metz (CoRR, 2021)

Mass Spectrometry Adduct Calculator. - Madison R. Blumer; Christine H. Chang; Evangelina Brayfindley; Jamie R. Nuñez; Sean M. Colby; Ryan S. Renslow; Thomas O. Metz (J. Chem. Inf. Model., 2021)

Correction to "Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets". - Jamie R. Nuñez; Monee Y. McGrady; Yasemin Yesiltepe; Ryan S. Renslow; Thomas O. Metz (J. Chem. Inf. Model., 2021)

AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry-mass spectrometry. - Joon-Yong Lee; Aivett Bilbao; Christopher R. Conant; Kent J. Bloodsworth; Daniel J. Orton; Mowei Zhou; Jesse William Wilson; Xueyun Zheng; Ian K. Webb; Ailin Li; Kim K. Hixson; John C. Fjeldsted; et al. (Bioinform., 2021)

An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts. - Yasemin Yesiltepe; Niranjan Govind; Thomas O. Metz; Ryan S. Renslow (J. Cheminformatics, 2022)

CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. - Fei Wang 062; Dana Allen; Siyang Tian; Eponine Oler; Vasuk Gautam; Russell Greiner; Thomas O. Metz; David S. Wishart (Nucleic Acids Res., 2022)

BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products. - David S. Wishart; Siyang Tian; Dana Allen; Eponine Oler; Harrison Peters; Vicki W. Lui; Vasuk Gautam; Yannick Djoumbou Feunang; Russell Greiner; Thomas O. Metz (Nucleic Acids Res., 2022)

DEIMoS GUI: An Open-Source User Interface for a High-Dimensional Mass Spectrometry Data Processing Tool. - Marjolein T. Oostrom; Sean M. Colby; Thomas O. Metz (J. Chem. Inf. Model., 2024)