{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T13:42:13Z","timestamp":1774878133815,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2023,10,27]],"date-time":"2023-10-27T00:00:00Z","timestamp":1698364800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01 CA235508"],"award-info":[{"award-number":["U01 CA235508"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The analysis of stable isotope labeling experiments requires accurate, efficient, and reproducible quantification of mass isotopomer distributions (MIDs), which is not a core feature of general-purpose metabolomics software tools that are optimized to quantify metabolite abundance. Here, we present PIRAMID (Program for Integration and Rapid Analysis of Mass Isotopomer Distributions), a MATLAB-based tool that addresses this need by offering a user-friendly, graphical user interface-driven program to automate the extraction of isotopic information from mass spectrometry (MS) datasets. This tool can simultaneously extract ion chromatograms for various metabolites from multiple data files in common vendor\u2013agnostic file formats, locate chromatographic peaks based on a targeted list of characteristic ions and retention times, and integrate MIDs for each target ion. These MIDs can be corrected for natural isotopic background based on the user-defined molecular formula of each ion. PIRAMID offers support for datasets acquired from low- or high-resolution MS, and single (MS) or tandem (MS\/MS) instruments. It also enables the analysis of single or dual labeling experiments using a variety of isotopes (i.e. 2H, 13C, 15N, 18O, 34S).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Data availability and implementation<\/jats:title>\n                  <jats:p>MATLAB p-code files are freely available for non-commercial use and can be downloaded from https:\/\/mfa.vueinnovations.com\/. Commercial licenses are also available. All the data presented in this publication are available under the \u201cHelp_menu\u201d folder of the PIRAMID software.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad661","type":"journal-article","created":{"date-parts":[[2023,10,25]],"date-time":"2023-10-25T20:55:35Z","timestamp":1698267335000},"source":"Crossref","is-referenced-by-count":13,"title":["Program for Integration and Rapid Analysis of Mass Isotopomer Distributions (PIRAMID)"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0871-1494","authenticated-orcid":false,"given":"Javier D","family":"Gomez","sequence":"first","affiliation":[{"name":"Department of Chemical and Biomolecular Engineering, Vanderbilt University , Nashville, TN, 37240, United States"}]},{"given":"Martha L","family":"Wall","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biomolecular Engineering, Vanderbilt University , Nashville, TN, 37240, United States"}]},{"given":"Mohsin","family":"Rahim","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biomolecular Engineering, Vanderbilt University , Nashville, TN, 37240, United States"}]},{"given":"Shrikaar","family":"Kambhampati","sequence":"additional","affiliation":[{"name":"Donald Danforth Plant Science Center , Olviette, MO, 63132, United States"}]},{"given":"Bradley S","family":"Evans","sequence":"additional","affiliation":[{"name":"Donald Danforth Plant Science Center , Olviette, MO, 63132, United States"}]},{"given":"Doug K","family":"Allen","sequence":"additional","affiliation":[{"name":"Donald Danforth Plant Science Center , Olviette, MO, 63132, United States"},{"name":"United States Department of Agriculture, Agricultural Research Service , Washington, DC, 20250, United States"}]},{"given":"Maciek R","family":"Antoniewicz","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA, 02139, United States"}]},{"given":"Jamey D","family":"Young","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biomolecular Engineering, Vanderbilt University , Nashville, TN, 37240, United States"},{"name":"Department of Molecular Physiology and Biophysics, Vanderbilt University , Nashville, TN, 37240, United States"}]}],"member":"286","published-online":{"date-parts":[[2023,10,27]]},"reference":[{"key":"2023111005481546700_btad661-B1","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1007\/978-1-4939-9236-2_19","article-title":"EL-MAVEN: a fast, robust, and user-friendly mass spectrometry data processing engine for metabolomics","volume":"1978","author":"Agrawal","year":"2019","journal-title":"Methods Mol Biol"},{"key":"2023111005481546700_btad661-B2","doi-asserted-by":"crossref","first-page":"7554","DOI":"10.1021\/ac0708893","article-title":"Accurate assessment of amino acid mass isotopomer distributions for metabolic flux 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