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class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/0rn2j1x1"><div class="c-clientmarkup">ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization.</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AShahneh%2C%20Mohammad">Shahneh, Mohammad</a>; </li><li><a href="/search/?q=author%3AStrobel%2C%20Michael">Strobel, Michael</a>; </li><li><a href="/search/?q=author%3AVitale%2C%20Giovanni">Vitale, Giovanni</a>; </li><li><a href="/search/?q=author%3AGeibel%2C%20Christian">Geibel, Christian</a>; </li><li><a href="/search/?q=author%3AAbiead%2C%20Yasin">Abiead, Yasin</a>; </li><li><a href="/search/?q=author%3AGarg%2C%20Neha">Garg, Neha</a>; </li><li><a href="/search/?q=author%3AWagner%2C%20Berenike">Wagner, Berenike</a>; </li><li><a href="/search/?q=author%3AForchhammer%2C%20Karl">Forchhammer, Karl</a>; </li><li><a href="/search/?q=author%3AAron%2C%20Allegra">Aron, Allegra</a>; </li><li><a href="/search/?q=author%3APhelan%2C%20Vanessa">Phelan, Vanessa</a>; </li><li><a href="/search/?q=author%3APetras%2C%20Daniel">Petras, Daniel</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AWang%2C%20Mingxun">Wang, Mingxun</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucr_postprints">UC Riverside Previously Published Works</a> (2024)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Untargeted tandem mass spectrometry (MS/MS) has become a high-throughput method to measure small molecules in complex samples. One key goal is the transformation of these MS/MS spectra into chemical structures. Computational techniques such as MS/MS library search have enabled the reidentification of known compounds. Analog library search and molecular networking extend this identification to unknown compounds. While there have been advancements in metrics for the similarity of MS/MS spectra of structurally similar compounds, there is still a lack of automated methods to provide site specific information about structural modifications. Here we introduce ModiFinder which leverages the alignment of peaks in MS/MS spectra between structurally related known and unknown small molecules. Specifically, ModiFinder focuses on shifted MS/MS fragment peaks in the MS/MS alignment. These shifted peaks putatively represent substructures of the known molecule that contain the site of the modification. ModiFinder synthesizes this information together and scores the likelihood for each atom in the known molecule to be the modification site. We demonstrate in this manuscript how ModiFinder can effectively localize modifications which extends the capabilities of MS/MS analog searching and molecular networking to accelerate the discovery of novel compounds.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/0rn2j1x1"><img src="/cms-assets/c235604219bcf524f0b6d403eb9467e766dbbdb07da04909302b1406d344bcb7" alt="Cover page: ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization."/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/4bq907gr"><div class="c-clientmarkup">Network Topology Evaluation and Transitive Alignments for Molecular Networking.</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AWang%2C%20Xianghu">Wang, Xianghu</a>; </li><li><a href="/search/?q=author%3AStrobel%2C%20Michael">Strobel, Michael</a>; </li><li><a href="/search/?q=author%3AAron%2C%20Allegra">Aron, Allegra</a>; </li><li><a href="/search/?q=author%3APhelan%2C%20Vanessa">Phelan, Vanessa</a>; </li><li><a href="/search/?q=author%3AAcharya%2C%20Deepa">Acharya, Deepa</a>; </li><li><a href="/search/?q=author%3ABrown%2C%20Christopher">Brown, Christopher</a>; </li><li><a href="/search/?q=author%3AClevenger%2C%20Ken">Clevenger, Ken</a>; </li><li><a href="/search/?q=author%3AHu%2C%20Jie">Hu, Jie</a>; </li><li><a href="/search/?q=author%3AKretsch%2C%20Ashley">Kretsch, Ashley</a>; </li><li><a href="/search/?q=author%3AMahood%2C%20Elizabeth">Mahood, Elizabeth</a>; </li><li><a href="/search/?q=author%3AMenegatti%2C%20Carla">Menegatti, Carla</a>; </li><li><a href="/search/?q=author%3AXiong%2C%20Quanbo">Xiong, Quanbo</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AWang%2C%20Mingxun">Wang, Mingxun</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucr_postprints">UC Riverside Previously Published Works</a> (2024)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Untargeted tandem mass spectrometry (MS/MS) is an essential technique in modern analytical chemistry, providing a comprehensive snapshot of chemical entities in complex samples and identifying unknowns through their fragmentation patterns. This high-throughput approach generates large data sets that can be challenging to interpret. Molecular Networks (MNs) have been developed as a computational tool to aid in the organization and visualization of complex chemical space in untargeted mass spectrometry data, thereby supporting comprehensive data analysis and interpretation. MNs group related compounds with potentially similar structures from MS/MS data by calculating all pairwise MS/MS similarities and filtering these connections to produce a MN. Such networks are instrumental in metabolomics for identifying novel metabolites, elucidating metabolic pathways, and even discovering biomarkers for disease. While MS/MS similarity metrics have been explored in the literature, the influence of network topology approaches on MN construction remains unexplored. This manuscript introduces metrics for evaluating MN construction, benchmarks state-of-the-art approaches, and proposes the Transitive Alignments approach to improve MN construction. The Transitive Alignment technique leverages the MN topology to realign MS/MS spectra of related compounds that differ by multiple structural modifications. Combining this Transitive Alignments approach with pseudoclique finding, a method for identifying highly connected groups of nodes in a network, resulted in more complete and higher-quality molecular families. Finally, we also introduce a targeted network construction technique called induced transitive alignments where we demonstrate effectiveness on a real world natural product discovery application. We release this transitive alignment technique as a high-throughput workflow that can be used by the wider research community.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/4bq907gr"><img src="/cms-assets/3c4b1e82cd5ad4c417fca078a358a53b34deb7596c0393d8eee7440c5f8125b0" alt="Cover page: Network Topology Evaluation and Transitive Alignments for Molecular Networking."/></a></div></section></section></main></form></div><div><div class="c-toplink"><a href="javascript:window.scrollTo(0, 0)">Top</a></div><footer class="c-footer"><nav class="c-footer__nav"><ul><li><a href="/">Home</a></li><li><a href="/aboutEschol">About eScholarship</a></li><li><a href="/campuses">Campus Sites</a></li><li><a href="/ucoapolicies">UC Open Access Policy</a></li><li><a href="/publishing">eScholarship Publishing</a></li><li><a href="https://www.cdlib.org/about/accessibility.html">Accessibility</a></li><li><a href="/privacypolicy">Privacy Statement</a></li><li><a href="/policies">Site Policies</a></li><li><a href="/terms">Terms of Use</a></li><li><a href="/login"><strong>Admin Login</strong></a></li><li><a href="https://help.escholarship.org"><strong>Help</strong></a></li></ul></nav><div class="c-footer__logo"><a href="/"><img class="c-lazyimage" data-src="/images/logo_footer-eschol.svg" alt="eScholarship, University of California"/></a></div><div class="c-footer__copyright">Powered by the<br/><a href="http://www.cdlib.org">California Digital Library</a><br/>Copyright 漏 2017<br/>The Regents of the University of California</div></footer></div></div></div></div> <script src="/js/vendors~app-bundle-2aefc956e545366a5d4e.js"></script> <script src="/js/app-bundle-3c8ebc2ec05dcc3202fd.js"></script> </body> </html>