More Like this

1. Application of chemical graph theory to PAH isomer enumeration and structure in laser desorption/ionization mass spectrometry studies of particulate from an ethylene diffusion flame

   https://doi.org/10.1016/j.proci.2020.06.080  

   Miller, J. Houston ; Golden, Rachelle J. ; Giaccai, Jennifer A. ; Kamischke, Andrew ; Korte, Andrew ; Vertes, Akos ( September 2020 , Proceedings of the Combustion Institute)
2. ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction

   https://doi.org/10.3390/metabo12121275  

   Quinlan, Zachary A. ; Koester, Irina ; Aron, Allegra T. ; Petras, Daniel ; Aluwihare, Lihini I. ; Dorrestein, Pieter C. ; Nelson, Craig E. ; Wegley Kelly, Linda ( December 2022 , Metabolites)

   Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications for entire subnetworks. By limiting annotation propagation to only structural classes which are identical for the majority of ion features within a subnetwork, ConCISE maintains a true positive rate greater than 95% across all levels of the ChemOnt hierarchical ontology used by the ClassyFire annotation software (superclass, class, subclass). The ConCISE framework expanded the proportion of reliable and consistent ion feature annotation up to 76%, allowing for improved assessment of the chemo-diversity of dissolved organic matter pools from three complex marine metabolomics datasets comprising dominant reef primary producers, five species of the diatom genus Pseudo-nitzchia, and stromatolite sediment samples. 

   more » « less
3. Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data

   https://doi.org/10.1021/acs.analchem.8b01624  

   Aprahamian, Melanie L. ; Chea, Emily E. ; Jones, Lisa M. ; Lindert, Steffen ( June 2018 , Analytical Chemistry)
4. Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

   https://doi.org/10.3791/60102  

   Yousef, Enas N. ; Sesham, Ramakrishna ; McCabe, Jacob W. ; Vangala, Rajpal ; Angel, Laurence A. ( January 2019 , Journal of Visualized Experiments)
5. Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling

   https://doi.org/10.1093/nar/gky125  

   Gadkari, Varun V ; Harvey, Sophie R ; Raper, Austin T ; Chu, Wen-Ting ; Wang, Jin ; Wysocki, Vicki H ; Suo, Zucai ( February 2018 , Nucleic Acids Research)