Publications

2022

Colby SM, Chang CH, Bade JL, Nunez JR, Blumer MR, Orton DJ, Bloodsworth KJ, Nakayasu ES, Smith RD, Ibrahim YM, Renslow RS, Metz TO. "DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data." Anal. Chem. 2022 Apr 26;94(16):6130-6138. doi: 10.1021/acs.analchem.1c05017

Farley SE, Kyle JE, Leier HC, Bramer LM, Weinstein JB, Bates TA, Lee JY, Metz TO, Schultz C, Tafesse FG. "A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants." Nature Communications. 2022 Jun 17;13(1):3487. doi: 10.1038/s41467-022-31097-7 - Awarded as top 1% of publications in Papers of the Year NIEHS and featured in EurekAlert.

Yesiltepe Y, Govind N, Metz TO, Renslow RS. J. "An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts." Journal of Cheminformatics 2022 Sep 22;14(1):64. doi: 10.1186/s13321-022-00587-7

2021

Lee JY, A Bilbao, CR Conant, KJ Bloodsworth, DJ Orton, M Zhou, JW Wilson, X Zheng, IK Webb, A Li, KK Hixson, JC Fjeldsted, YM Ibrahim, SH Payne, C Jansson, RD Smith, TO Metz. "AutoCCS: Automated collision cross section calculation software for ion mobility spectrometry-mass spectrometry." Bioinformatics. 2021 Jun 18:btab429. doi: 10.1093/bioinformatics/btab429. Online ahead of print. PMID: 34145874

Blumer MR, CH Chang, E Brayfindley, J Nunez, SM Colby, RS Renslow, and TO Metz. 2021. "Mass Spectrometry Adduct Calculator." Journal of Cheminformatics and Modeling 2021. PNNL-SA-162668. doi/10.1021/acs.jcim.1c00579

Wang F, J Liigand, S Tian, D Arndt, R Greiner, and D Wishart. 2021. "CFM-ID 4.0: More Accurate ESI MS/MS Spectral Prediction and Compound Identification." Analytical Chemistry 93, no. 34:11692–11700. PNNL-SA-160966. doi:10.1021/acs.analchem.1c01465

Tian S, X Cao, R Greiner, C Li, A Guo, and D Wishart. 2021. "CyProduct: A software tool for accurately predicting the byproducts of human cytochrome P450 metabolism." Journal of Chemical Information and Modeling 61, no. 6:3128-3140. PNNL-SA-160965. doi:10.1021/acs.jcim.1c00144

Borges RM, SM Colby, S Das, A Edison, ON Fiehn, T Kind, and J Lee, et al. 2021. "Quantum chemistry calculations for metabolomics." Chemical Reviews 121, no. 10:5633-5670. PNNL-SA-155806. doi:10.1021/acs.chemrev.0c00901

Nielson FF, SM Colby, DG Thomas, RS Renslow*, and TO Metz*. 2021. "Exploring the Impacts of Conformer Selection Methods on Ion Mobility Collision Cross Section Predictions." Anal Chem 93(8):3830-3838. https://doi.org/10.1021/acs.analchem.0c04341

Barklis EW, A Alfadhli, JE Kyle, LM Bramer, KJ Bloodsworth, R Lid Barklis, and HC Leier, et al. 2021. "Ceramide Synthase 2 Deletion Decreases the Infectivity of HIV-1." Journal of Biological Chemistry 296. PNNL-SA-156982. doi:10.1016/j.jbc.2021.100340

2020

Chang HY, SM Colby, X Du, JD Gomez, MJ Helf, K Kechris, CR Kirkpatrick, S Li, GJ Patti, RS Renslow, S Subramaniam, M Verma, J Xia, JD Young. 2020. "A Practical Guide to Metabolomics Software Development." Anal Chem. doi: https://doi.org/10.1021/acs.analchem.0c03581

Nuñez JR, M McGrady, Y Yesiltepe, RS Renslow, and TO Metz. 2020. "Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets." J Chem Inf Model. 60(12):6251-6257. https://doi.org/10.1021/acs.jcim.0c00899

Couvillion SP, N Agrawal, SM Colby, KR Brandvold, and TO Metz. 2020. "Who is Metabolizing What? Discovering Novel Biomolecules in the Microbiome and the Organisms Who Make Them." Front Cell Infect Microbiol. 10:388. https://doi.org/10.3389/fcimb.2020.00388

Wojcik R, GNagy, IK Attah, IK Webb, SVB Garimella, KK Weitz, A Hollerbach, ME Monroe, MR Ligare, FF Nielson, RV Norheim, RS Renslow, TO Metz, YM Ibrahim, and RD Smith*. 2019. "SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes." Anal. Chem. 91(18):11952-11962. https://doi.org/10.1021/acs.analchem.9b02808 

Nuñez JR, SM Colby, DG Thomas, MM Tfaily, N Tolic, EM Ulrich, JR Sobus, TO Metz*, JG Teeguarden*, R Renslow*. 2019. "Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples." J. Chem. Inf. Model. 59(9):4052-4060. https://doi.org/10.1021/acs.jcim.9b00444

Colby SM, DG Thomas, JR Nuñez, DJ Baxter, KR Glaesemann, JM Brown, MA Pirrung, N Govind, JG Teeguarden, TO Metz*, RS Renslow*. 2019. "ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries." Anal. Chem. 91(7):4346-4356. https://doi.org/10.1021/acs.analchem.8b04567

Couvillion SP, Y Zhu, G Nagy, JN Adkins, C Ansong, RS Renslow, PD Piehowski, YM Ibrahim, RT Kelly, TO Metz*. 2019. "New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells." Analyst 144:794-807. https://doi.org/10.1039/C8AN01574K