{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T08:10:23Z","timestamp":1774944623533,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,2,20]],"date-time":"2025-02-20T00:00:00Z","timestamp":1740009600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Untargeted metabolomics involves a large-scale comparison of the fragmentation pattern of a mass spectrum against a database containing known spectra. Given the number of comparisons involved, this step can be time-consuming.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this work, we present a GPU-accelerated cosine similarity implementation for Tandem Mass Spectrometry (MS), with an approximately 1000-fold speedup compared to the MatchMS reference implementation, without any loss of accuracy. This improvement enables repository-scale spectral library matching for compound identification without the need for large compute clusters. This impact extends to any spectral comparison-based methods such as molecular networking approaches and analogue search.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>All code, results, and notebooks supporting are freely available under the MIT license at https:\/\/github.com\/pangeAI\/simms\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf081","type":"journal-article","created":{"date-parts":[[2025,2,18]],"date-time":"2025-02-18T07:19:00Z","timestamp":1739863140000},"source":"Crossref","is-referenced-by-count":4,"title":["SimMS: a GPU-accelerated cosine similarity implementation for tandem mass spectrometry"],"prefix":"10.1093","volume":"41","author":[{"given":"Tornike","family":"Onoprishvili","sequence":"first","affiliation":[{"name":"Independent Consultant"}]},{"given":"Jui-Hung","family":"Yuan","sequence":"additional","affiliation":[{"name":"Pangea Botanica Germany GmbH , Berlin 10623,","place":["Germany"]}]},{"given":"Kamen","family":"Petrov","sequence":"additional","affiliation":[{"name":"Pangea Botanica Germany GmbH , Berlin 10623,","place":["Germany"]}]},{"given":"Vijay","family":"Ingalalli","sequence":"additional","affiliation":[{"name":"Pangea Botanica Germany GmbH , Berlin 10623,","place":["Germany"]}]},{"given":"Lila","family":"Khederlarian","sequence":"additional","affiliation":[{"name":"Pangea Botanica Ltd , London WC1A 2AJ,","place":["United Kingdom"]}]},{"given":"Niklas","family":"Leuchtenmuller","sequence":"additional","affiliation":[{"name":"Wilde Ventures GmbH , D\u00fcsseldorf 40629,","place":["Germany"]}]},{"given":"Sona","family":"Chandra","sequence":"additional","affiliation":[{"name":"Pangea Botanica Germany GmbH , Berlin 10623,","place":["Germany"]}]},{"given":"Aurelien","family":"Duarte","sequence":"additional","affiliation":[{"name":"Independent Consultant"}]},{"given":"Andreas","family":"Bender","sequence":"additional","affiliation":[{"name":"Pangea Botanica Germany GmbH , Berlin 10623,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0493-8592","authenticated-orcid":false,"given":"Yoann","family":"Gloaguen","sequence":"additional","affiliation":[{"name":"Pangea Botanica Germany GmbH , Berlin 10623,","place":["Germany"]}]}],"member":"286","published-online":{"date-parts":[[2025,2,20]]},"reference":[{"key":"2025030711571943200_btaf081-B1","doi-asserted-by":"crossref","first-page":"8488","DOI":"10.1038\/s41467-023-44035-y","article-title":"Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics","volume":"14","author":"Bittremieux","year":"2023","journal-title":"Nat 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