{"id":426,"date":"2020-04-29T22:15:44","date_gmt":"2020-04-29T22:15:44","guid":{"rendered":"http:\/\/bile.ucsd.edu\/?page_id=426"},"modified":"2026-10-07T00:14:48","modified_gmt":"2026-10-07T00:14:48","slug":"resources","status":"publish","type":"page","link":"https:\/\/bile.ucsd.edu\/?page_id=426","title":{"rendered":"Resources"},"content":{"rendered":"\n<style>\n.ba-res{max-width:820px;margin:0 auto 40px}\n.ba-res h2{font-size:24px;font-weight:600;margin:36px 0 6px}\n.ba-res .lead{color:#555;margin:0 0 18px}\n.ba-res ol.pubs{padding-left:1.4em;margin:0}\n.ba-res ol.pubs li{margin:0 0 14px;line-height:1.55}\n.ba-res ol.pubs .t{font-weight:600}\n.ba-res a{color:#2f6f6a}\n.ba-res .tools{display:grid;grid-template-columns:repeat(2,minmax(0,1fr));gap:16px}\n.ba-res .tool{background:#fff;border:1px solid #d5e3e1;border-left:4px solid #2f6f6a;border-radius:10px;padding:14px 16px}\n.ba-res .tool h3{font-size:17px;margin:0 0 2px}\n.ba-res .tag{display:inline-block;font-size:11px;text-transform:uppercase;letter-spacing:.8px;color:#2f6f6a;background:#e7f1f0;border-radius:999px;padding:2px 9px;margin:0 0 8px}\n.ba-res .tool p{margin:0 0 8px;font-size:14px;line-height:1.5}\n.ba-res .links a{display:inline-block;margin:0 8px 6px 0;font-size:13px;font-weight:600;border:1.5px solid #2f6f6a;border-radius:999px;padding:3px 12px;text-decoration:none}\n.ba-res .links a:hover{background:#2f6f6a;color:#fff}\n.ba-res .cite{font-size:12px;color:#666;margin:4px 0 0}\n.ba-res .updated{text-align:right;font-size:12px;color:#777;font-style:italic;margin-top:30px}\n@media (max-width:640px){.ba-res .tools{grid-template-columns:1fr}}\n<\/style>\n<div class=\"ba-res\">\n<p class=\"lead\">Selected publications, software and spectral libraries for studying bile acids by mass spectrometry.<\/p>\n<h2>Publications from the Dorrestein Lab<\/h2>\n<p class=\"lead\">Recent work on bile acid discovery and annotation, newest first.<\/p>\n<ol class=\"pubs\">\n<li>Mohanty I, Xing S, Castillo V, <em>et al.<\/em> <span class=\"t\">MS\/MS mass spectrometry filtering tree for bile acid regio- and stereoisomer annotation.<\/span> <em>Analytical Chemistry<\/em> 98(6):4571\u20134584 (2026). <a href=\"https:\/\/doi.org\/10.1021\/acs.analchem.5c05677\" target=\"_blank\" rel=\"noopener\">doi:10.1021\/acs.analchem.5c05677<\/a><\/li>\n<li>Mohanty I, Allaband C, Mannochio-Russo H, El Abiead Y, Hagey LR, Knight R, Dorrestein PC. <span class=\"t\">The changing metabolic landscape of bile acids \u2013 keys to metabolism and immune regulation.<\/span> <em>Nature Reviews Gastroenterology &amp; Hepatology<\/em> 21(7):493\u2013516 (2024). <a href=\"https:\/\/doi.org\/10.1038\/s41575-024-00914-3\" target=\"_blank\" rel=\"noopener\">doi:10.1038\/s41575-024-00914-3<\/a><\/li>\n<li>Mohanty I, Mannochio-Russo H, Schweer JV, <em>et al.<\/em> <span class=\"t\">The underappreciated diversity of bile acid modifications.<\/span> <em>Cell<\/em> 187(7):1801\u20131818.e20 (2024). <a href=\"https:\/\/doi.org\/10.1016\/j.cell.2024.02.019\" target=\"_blank\" rel=\"noopener\">doi:10.1016\/j.cell.2024.02.019<\/a><\/li>\n<li>Gentry EC, Collins SL, Panitchpakdi M, <em>et al.<\/em> <span class=\"t\">Reverse metabolomics for the discovery of chemical structures from humans.<\/span> <em>Nature<\/em> 626(7998):419\u2013426 (2024). <a href=\"https:\/\/doi.org\/10.1038\/s41586-023-06906-8\" target=\"_blank\" rel=\"noopener\">doi:10.1038\/s41586-023-06906-8<\/a><\/li>\n<li>Quinn RA, <em>et al.<\/em> <span class=\"t\">Global chemical effects of the microbiome include new bile-acid conjugations.<\/span> <em>Nature<\/em> 579:123\u2013129 (2020). <a href=\"https:\/\/doi.org\/10.1038\/s41586-020-2047-9\" target=\"_blank\" rel=\"noopener\">doi:10.1038\/s41586-020-2047-9<\/a><\/li>\n<\/ol>\n<h2>Computational Tools &amp; Libraries for Bile Acid Annotation<\/h2>\n<p class=\"lead\">Free tools and reference spectra for finding and annotating bile acids in untargeted LC-MS\/MS data.<\/p>\n<div class=\"tools\">\n<div class=\"tool\"><span class=\"tag\">Web app<\/span><h3>Multistep MassQL \u2013 Bile Acid Isomer Annotation<\/h3><p>Runs a sequence of MassQL filters on untargeted LC-MS\/MS data to narrow bile acid MS\/MS spectra down to likely regio- and stereoisomers.<\/p><div class=\"links\"><a href=\"https:\/\/multistep-massql.gnps2.org\/\" target=\"_blank\" rel=\"noopener\">Open the app<\/a><a href=\"https:\/\/github.com\/wilhan-nunes\/streamlit-Multi-Step-MassQL\" target=\"_blank\" rel=\"noopener\">Source code<\/a><a href=\"https:\/\/github.com\/mohantyipsita\/MassQL_bile_Acid_isomer_2025\" target=\"_blank\" rel=\"noopener\">MassQL queries<\/a><\/div><p class=\"cite\">Mohanty <em>et al.<\/em>, <em>Anal. Chem.<\/em> 2026 \u2013 <a href=\"https:\/\/doi.org\/10.1021\/acs.analchem.5c05677\" target=\"_blank\" rel=\"noopener\">doi:10.1021\/acs.analchem.5c05677<\/a><\/p><\/div>\n<div class=\"tool\"><span class=\"tag\">Web app<\/span><h3>PostMN MassQL (MetaboApps)<\/h3><p>Runs after molecular networking in GNPS2 and flags bile acid patterns with different numbers of hydroxyl groups across the network.<\/p><div class=\"links\"><a href=\"https:\/\/massqlpostmn.gnps2.org\/\" target=\"_blank\" rel=\"noopener\">Open the app<\/a><a href=\"https:\/\/github.com\/helenamrusso\/massql_post_MN\" target=\"_blank\" rel=\"noopener\">Source code<\/a><\/div><p class=\"cite\">Mannochio-Russo, Gon\u00e7alves Nunes <em>et al.<\/em>, <em>Nature Methods<\/em> 23:1475\u20131477 (2026) \u2013 <a href=\"https:\/\/doi.org\/10.1038\/s41592-026-03186-8\" target=\"_blank\" rel=\"noopener\">doi:10.1038\/s41592-026-03186-8<\/a>; preprint: <a href=\"https:\/\/doi.org\/10.26434\/chemrxiv-2025-3nq29\" target=\"_blank\" rel=\"noopener\">ChemRxiv 2025<\/a><\/p><\/div>\n<div class=\"tool\"><span class=\"tag\">GNPS library<\/span><h3>BILELIB19 spectral library<\/h3><p>A reference library of 21,549 bile acid MS\/MS spectra for library searches and molecular networking in GNPS.<\/p><div class=\"links\"><a href=\"https:\/\/gnps.ucsd.edu\/ProteoSAFe\/gnpslibrary.jsp?library=BILELIB19\" target=\"_blank\" rel=\"noopener\">View library<\/a><\/div><\/div>\n<div class=\"tool\"><span class=\"tag\">GNPS library<\/span><h3>GNPS-MASSQL-BILE-ACID-ISOMER library<\/h3><p>911 bile acid spectra with assigned regio- and stereochemistry, built using the filtering tree above.<\/p><div class=\"links\"><a href=\"https:\/\/gnps.ucsd.edu\/ProteoSAFe\/gnpslibrary.jsp?library=GNPS-MASSQL-BILE-ACID-ISOMER\" target=\"_blank\" rel=\"noopener\">View library<\/a><\/div><p class=\"cite\">Mohanty <em>et al.<\/em>, <em>Anal. Chem.<\/em> 2026<\/p><\/div>\n<div class=\"tool\"><span class=\"tag\">Query language<\/span><h3>MassQL<\/h3><p>A language for searching mass spectrometry data for patterns such as fragment ions and neutral losses. It powers the bile acid filters above.<\/p><p class=\"cite\">Damiani T, Jarmusch AK, Aron AT, <em>et al.<\/em>, <em>Nature Methods<\/em> 22(6):1247\u20131254 (2025) \u2013 <a href=\"https:\/\/doi.org\/10.1038\/s41592-025-02660-z\" target=\"_blank\" rel=\"noopener\">doi:10.1038\/s41592-025-02660-z<\/a><\/p><\/div>\n<div class=\"tool\"><span class=\"tag\">Platform<\/span><h3>GNPS2<\/h3><p>Molecular networking, spectral library search and MASST searches across public data, plus the MetaboApps for downstream analysis.<\/p><div class=\"links\"><a href=\"https:\/\/gnps2.org\/\" target=\"_blank\" rel=\"noopener\">Go to GNPS2<\/a><\/div><\/div>\n<div class=\"tool\"><span class=\"tag\">Library \u2013 external<\/span><h3>Multidimensional bile acid library (LC-IMS-MS)<\/h3><p>Retention times, collision cross sections and accurate masses for 280 bile acids, from a group outside UC San Diego.<\/p><div class=\"links\"><a href=\"https:\/\/doi.org\/10.5281\/zenodo.18675023\" target=\"_blank\" rel=\"noopener\">Zenodo dataset<\/a><\/div><p class=\"cite\">Zhang G, Vincent EC, Disselkoen SM, <em>et al.<\/em>, bioRxiv preprint (2026) \u2013 <a href=\"https:\/\/doi.org\/10.64898\/2026.02.18.706700\" target=\"_blank\" rel=\"noopener\">doi:10.64898\/2026.02.18.706700<\/a><\/p><\/div>\n<\/div>\n<p class=\"updated\">Last updated: October 6, 2026<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Selected publications, software and spectral libraries for studying bile acids by mass spectrometry. Publications from the Dorrestein Lab Recent work on bile acid discovery and annotation, newest first. Mohanty I, Xing S, Castillo V, et al. MS\/MS mass spectrometry filtering &hellip; <a href=\"https:\/\/bile.ucsd.edu\/?page_id=426\">Continued<\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"kt_blocks_editor_width":"","footnotes":""},"class_list":["post-426","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/bile.ucsd.edu\/index.php?rest_route=\/wp\/v2\/pages\/426","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bile.ucsd.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bile.ucsd.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bile.ucsd.edu\/index.php?rest_route=\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/bile.ucsd.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=426"}],"version-history":[{"count":3,"href":"https:\/\/bile.ucsd.edu\/index.php?rest_route=\/wp\/v2\/pages\/426\/revisions"}],"predecessor-version":[{"id":616,"href":"https:\/\/bile.ucsd.edu\/index.php?rest_route=\/wp\/v2\/pages\/426\/revisions\/616"}],"wp:attachment":[{"href":"https:\/\/bile.ucsd.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=426"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}