{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T12:51:06Z","timestamp":1791895866340,"version":"4.3.4"},"reference-count":43,"publisher":"American Chemical Society (ACS)","issue":"40","license":[{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/na","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["32571674"],"award-info":[{"award-number":["32571674"]}],"id":[{"id":"10.13039\/na","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Ribonucleic acid (RNA) modifications, with over 170 identified types, play diverse roles in cellular processes. The past decade has witnessed a surging demand for accurate identification and localization of RNA modifications in both endogenous and synthetic therapeutic RNAs. With accurate spectral annotation for RNA, tandem mass spectrometry (MS\/MS) can meet this demand. Here, we present RNabel, a user-friendly software tool for in-depth annotation of MS\/MS spectra of RNA oligonucleotides. RNabel considers a full set of backbone-cleavage ions (a, b, c, d, a-B, w, x, y, z) in which the ribonucleotide unit could be A, U, C, G, Y (pseudouridine), or I (Inosine). Additionally, RNabel considers 196 modifications on the base, the phosphoribose linkage, the 5\u2032 or the 3\u2032 terminus, or the detachment of a subnucleotide fragment as a neutral or charged group. Users can create new components if needed, including ribonucleotides, modifications, and neutral or charged groups that could detach from a ribonucleotide. RNabel efficiently processes large data sets in four acceptable formats including .mgf, .raw, .txt from msConvert, and RNabel batch files. Multiple statistical metrics are provided for quality assessment of spectral annotation. To accelerate RNA modification analysis, RNabel is made freely available for Mac and Windows users at https:\/\/github.com\/songge1111\/RNabel\/releases.<\/jats:p>","DOI":"10.1021\/acs.analchem.6c02176","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T06:01:43Z","timestamp":1790575303000},"page":"29188-29201","source":"Crossref","is-referenced-by-count":0,"title":["RNabel\u2500A\nStandalone Software Tool for Annotating\nTandem Mass Spectra of Modified Ribonucleic Acids"],"prefix":"10.1021","volume":"98","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-1449-0079","authenticated-orcid":true,"given":"Ge","family":"Song","sequence":"first","affiliation":[{"name":"Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences , ,","place":["Beijing, China, 100730"]},{"name":"National Institute of Biological Sciences , ,","place":["Beijing, China, 102206"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Jie Nathan","family":"Du","sequence":"additional","affiliation":[{"name":"Goldsmiths, University of London , , Lewisham Way, New Cross , ,","place":["London, U.K., SE14 6NW"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7540-5131","authenticated-orcid":true,"given":"Rui-Xiang","family":"Sun","sequence":"additional","affiliation":[{"name":"National Institute of Biological Sciences , ,","place":["Beijing, China, 102206"]},{"name":"Tsinghua University , , ,","place":["Beijing, China, 100084"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6094-1182","authenticated-orcid":true,"given":"Meng-Qiu","family":"Dong","sequence":"additional","affiliation":[{"name":"National Institute of Biological Sciences , ,","place":["Beijing, China, 102206"]},{"name":"Tsinghua University , , ,","place":["Beijing, China, 100084"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,28]]},"reference":[{"issue":"7","key":"2026101308070478600_cit1","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1016\/j.cell.2017.05.045","article-title":"Dynamic RNA Modifications\nin Gene Expression Regulation","volume":"169","author":"Roundtree","year":"2017","journal-title":"Cell"},{"issue":"5","key":"2026101308070478600_cit2","doi-asserted-by":"publisher","DOI":"10.1002\/wrna.1595","article-title":"Naturally Occurring\nModified Ribonucleosides","volume":"11","author":"McCown","year":"2020","journal-title":"Wiley Interdiscip.\nRev.: RNA"},{"issue":"8","key":"2026101308070478600_cit3","doi-asserted-by":"publisher","first-page":"1227","DOI":"10.1042\/BCJ20180445","article-title":"The Chemical Diversity of RNA Modifications","volume":"476","author":"Ontiveros","year":"2019","journal-title":"Biochem. J."},{"issue":"9","key":"2026101308070478600_cit4","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1016\/j.tibs.2021.02.002","article-title":"ADAR RNA Modifications, the Epitranscriptome and Innate\nImmunity","volume":"46","author":"Quin","year":"2021","journal-title":"Trends Biochem. Sci."},{"issue":"12","key":"2026101308070478600_cit5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005687","article-title":"The Epitranscriptome\nand Innate Immunity","volume":"11","author":"O\u2019connell","year":"2015","journal-title":"PLoS Genet."},{"issue":"6409","key":"2026101308070478600_cit6","doi-asserted-by":"publisher","first-page":"1346","DOI":"10.1126\/science.aau1646","article-title":"RNA Modifications Modulate\nGene Expression during Development","volume":"361","author":"Frye","year":"2018","journal-title":"Science"},{"issue":"6","key":"2026101308070478600_cit7","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1038\/s41568-020-0253-2","article-title":"Role of RNA Modifications in Cancer","volume":"20","author":"Barbieri","year":"2020","journal-title":"Nat. Rev. Cancer"},{"issue":"6","key":"2026101308070478600_cit8","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1016\/j.molmed.2014.01.008","article-title":"Role of tRNA Modifications in Human\nDiseases","volume":"20","author":"Torres","year":"2014","journal-title":"Trends Mol. Med."},{"issue":"2","key":"2026101308070478600_cit9","doi-asserted-by":"publisher","first-page":"70","DOI":"10.52601\/bpr.2025.250002","article-title":"Global Research\nTrends on the Relationship\nbetween RNA m5C Modification and Cancer Progression: A Comprehensive\nVisualization and Bibliometric Analysis (1900\u20132024)","volume":"12","author":"Yao","year":"2026","journal-title":"Biophys. Rep."},{"issue":"6","key":"2026101308070478600_cit10","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1016\/j.molcel.2019.03.040","article-title":"METTL1\nPromotes Let-7 MicroRNA Processing via\nm7G Methylation","volume":"74","author":"Pandolfini","year":"2019","journal-title":"Mol. Cell"},{"issue":"17","key":"2026101308070478600_cit11","doi-asserted-by":"publisher","first-page":"5884","DOI":"10.1093\/nar\/gkq347","article-title":"Incorporation\nof Pseudouridine into mRNA Enhances Translation by Diminishing PKR\nActivation","volume":"38","author":"Anderson","year":"2010","journal-title":"Nucleic Acids Res."},{"issue":"11","key":"2026101308070478600_cit12","doi-asserted-by":"publisher","first-page":"1833","DOI":"10.1038\/mt.2008.200","article-title":"Incorporation of Pseudouridine into\nmRNA Yields Superior Nonimmunogenic Vector with Increased Translational\nCapacity and Biological Stability","volume":"16","author":"Kariko\u0301","year":"2008","journal-title":"Mol. Ther."},{"issue":"2","key":"2026101308070478600_cit13","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/j.immuni.2005.06.008","article-title":"Suppression of RNA\nRecognition by Toll-like Receptors: The Impact of Nucleoside Modification\nand the Evolutionary Origin of RNA","volume":"23","author":"Kariko\u0301","year":"2005","journal-title":"Immunity"},{"issue":"7","key":"2026101308070478600_cit14","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1016\/j.cell.2012.05.003","article-title":"Comprehensive Analysis of mRNA Methylation Reveals\nEnrichment in 3\u2032 UTRs and near Stop Codons","volume":"149","author":"Meyer","year":"2012","journal-title":"Cell"},{"issue":"11","key":"2026101308070478600_cit15","doi-asserted-by":"publisher","first-page":"2024","DOI":"10.1038\/s41592-024-02439-8","article-title":"Absolute\nQuantitative and Base-Resolution Sequencing Reveals Comprehensive\nLandscape of Pseudouridine across the Human Transcriptome","volume":"21","author":"Xu","year":"2024","journal-title":"Nat. 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Commun."},{"issue":"sup1","key":"2026101308070478600_cit18","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1080\/15476286.2021.1978215","article-title":"Computational Methods for RNA Modification\nDetection from Nanopore Direct RNA Sequencing Data","volume":"18","author":"Furlan","year":"2021","journal-title":"RNA Biol."},{"issue":"12","key":"2026101308070478600_cit19","doi-asserted-by":"publisher","first-page":"3434","DOI":"10.1016\/j.jprot.2012.01.032","article-title":"Mass Spectrometry in\nthe Biology of RNA and Its Modifications","volume":"75","author":"Giessing","year":"2012","journal-title":"J.\nProteomics"},{"issue":"1","key":"2026101308070478600_cit20","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1021\/acs.analchem.8b04078","article-title":"Analytical Methods\nfor Deciphering\nRNA Modifications","volume":"91","author":"Chen","year":"2019","journal-title":"Anal. Chem."},{"issue":"1","key":"2026101308070478600_cit21","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/S0021-9673(97)00902-3","article-title":"Liquid Chromatography\u2013Mass\nSpectrometry in Nucleoside,\nNucleotide and Modified Nucleotide Characterization","volume":"794","author":"Esmans","year":"1998","journal-title":"J. Chromatogr. A"},{"issue":"12","key":"2026101308070478600_cit22","doi-asserted-by":"publisher","first-page":"1832","DOI":"10.1016\/j.jasms.2008.08.009","article-title":"Ion Trap Collision-Induced\nDissociation of Multiply Deprotonated RNA: C\/y-Ions versus (a-B)\/w-Ions","volume":"19","author":"Huang","year":"2008","journal-title":"J. Am. Soc. 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Soc.\nMass Spectrom."},{"issue":"8","key":"2026101308070478600_cit25","doi-asserted-by":"publisher","first-page":"1262","DOI":"10.1016\/j.jasms.2005.03.024","article-title":"Gas-Phase Dissociation of Oligoribonucleotides\nand\nTheir Analogs Studied by Electrospray Ionization Tandem Mass Spectrometry","volume":"16","author":"Tromp","year":"2005","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"10","key":"2026101308070478600_cit26","doi-asserted-by":"publisher","first-page":"1353","DOI":"10.1016\/j.jasms.2006.05.018","article-title":"RNA Fragmentation\nin MALDI Mass Spectrometry\nStudied by H\/D-Exchange: Mechanisms of General Applicability to Nucleic\nAcids","volume":"17","author":"Andersen","year":"2006","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"1","key":"2026101308070478600_cit27","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1038\/s41467-020-14665-7","article-title":"A Computational\nPlatform for High-Throughput Analysis of RNA Sequences and Modifications\nby Mass Spectrometry","volume":"11","author":"Wein","year":"2020","journal-title":"Nat. Commun."},{"issue":"1","key":"2026101308070478600_cit28","doi-asserted-by":"publisher","first-page":"2424","DOI":"10.1038\/s41467-022-30057-5","article-title":"Pytheas:\nA Software Package for the Automated Analysis\nof RNA Sequences and Modifications via Tandem Mass Spectrometry","volume":"13","author":"D\u2019ascenzo","year":"2022","journal-title":"Nat. Commun."},{"issue":"6","key":"2026101308070478600_cit29","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp099","article-title":"Ariadne: A Database\nSearch Engine for Identification and Chemical Analysis of RNA Using\nTandem Mass Spectrometry Data","volume":"37","author":"Nakayama","year":"2009","journal-title":"Nucleic Acids\nRes."},{"issue":"20","key":"2026101308070478600_cit30","doi-asserted-by":"publisher","first-page":"10744","DOI":"10.1021\/acs.analchem.7b01780","article-title":"RNAModMapper: RNA\nModification Mapping Software for Analysis of Liquid Chromatography\nTandem Mass Spectrometry Data","volume":"89","author":"Yu","year":"2017","journal-title":"Anal. Chem."},{"issue":"2","key":"2026101308070478600_cit31","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1007\/s13361-012-0529-1","article-title":"OMA and OPA\u2500Software-Supported\nMass Spectra Analysis of Native and Modified Nucleic Acids","volume":"24","author":"Nyakas","year":"2013","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"10","key":"2026101308070478600_cit32","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv145","article-title":"RoboOligo: Software\nfor Mass Spectrometry Data to Support Manual and de Novo Sequencing\nof Post-Transcriptionally Modified Ribonucleic Acids","volume":"43","author":"Sample","year":"2015","journal-title":"Nucleic Acids Res."},{"issue":"23","key":"2026101308070478600_cit33","doi-asserted-by":"publisher","DOI":"10.1002\/rcm.8927","article-title":"Aom2S: A New Web-Based\nApplication for DNA\/RNA Tandem Mass Spectrometry\nData Interpretation","volume":"34","author":"Ortiz","year":"2020","journal-title":"Rapid Commun. Mass Spectrom."},{"issue":"2","key":"2026101308070478600_cit34","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1021\/jasms.4c00236","article-title":"FAST MS: Software for\nthe Automated Analysis of Top-Down\nMass Spectra of Polymeric Molecules Including RNA, DNA, and Proteins","volume":"36","author":"Palasser","year":"2025","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"8","key":"2026101308070478600_cit35","doi-asserted-by":"publisher","first-page":"1598","DOI":"10.1021\/jasms.3c00073","article-title":"Charge-State-Dependent\nCollision-Induced Dissociation Behaviors of RNA Oligonucleotides via\nHigh-Resolution Mass Spectrometry","volume":"34","author":"Sun","year":"2023","journal-title":"J. Am. Soc.\nMass Spectrom."},{"issue":"3","key":"2026101308070478600_cit36","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1016\/j.jasms.2005.12.001","article-title":"Efficient Calculation\nof Accurate Masses of Isotopic Peaks","volume":"17","author":"Rockwood","year":"2006","journal-title":"J. Am.\nSoc. Mass Spectrom."},{"issue":"13","key":"2026101308070478600_cit37","doi-asserted-by":"publisher","first-page":"2027","DOI":"10.1021\/ac951158i","article-title":"Ultrahigh-Speed Calculation of Isotope\nDistributions","volume":"68","author":"Rockwood","year":"1996","journal-title":"Anal. Chem."},{"issue":"4","key":"2026101308070478600_cit38","doi-asserted-by":"publisher","first-page":"100742","DOI":"10.1016\/j.mcpro.2024.100742","article-title":"Phosphorothioate\nRNA Analysis by NETD Tandem Mass Spectrometry","volume":"23","author":"Peters-Clarke","year":"2024","journal-title":"Mol. Cell. Proteomics"},{"issue":"3","key":"2026101308070478600_cit39","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1021\/jasms.1c00340","article-title":"Ultraviolet Photodissociation and Activated Electron\nPhotodetachment Mass Spectrometry for Top-Down Sequencing of Modified\nOligoribonucleotides","volume":"33","author":"Santos","year":"2022","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"4","key":"2026101308070478600_cit40","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1016\/j.jasms.2009.12.011","article-title":"Infrared Multiphoton Dissociation\nof Small-Interfering RNA Anions and Cations","volume":"21","author":"Gardner","year":"2010","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"35","key":"2026101308070478600_cit41","doi-asserted-by":"publisher","first-page":"12742","DOI":"10.1073\/pnas.0800445105","article-title":"Determination\nof Pyrophosphorylated Forms of Lipid A in Gram-Negative Bacteria Using\na Multivaried Mass Spectrometric Approach","volume":"105","author":"Jones","year":"2008","journal-title":"Proc.\nNatl. Acad. Sci. U. S. A."},{"issue":"4","key":"2026101308070478600_cit42","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1016\/1044-0305(95)00017-8","article-title":"Determination\nof Monoisotopic Masses\nand Ion Populations for Large Biomolecules from Resolved Isotopic\nDistributions","volume":"6","author":"Senko","year":"1995","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"15","key":"2026101308070478600_cit43","doi-asserted-by":"publisher","first-page":"4687","DOI":"10.1021\/ac058023p","article-title":"Detection of the Common RNA Nucleoside Pseudouridine\nin Mixtures of Oligonucleotides by Mass Spectrometry","volume":"77","author":"Pomerantz","year":"2005","journal-title":"Anal. Chem."}],"container-title":["Analytical Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.analchem.6c02176","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/ancham\/article-pdf\/98\/40\/29188\/68671471\/acs.analchem.6c02176.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/ancham\/article-pdf\/98\/40\/29188\/68671471\/acs.analchem.6c02176.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T12:12:49Z","timestamp":1791893569000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/ancham\/article\/98\/40\/29188\/5439638\/RNabel-A-Standalone-Software-Tool-for-Annotating"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,28]]},"references-count":43,"journal-issue":{"issue":"40","published-online":{"date-parts":[[2026,9,28]]},"published-print":{"date-parts":[[2026,10,13]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.analchem.6c02176","relation":{},"ISSN":["0003-2700","1520-6882"],"issn-type":[{"value":"0003-2700","type":"print"},{"value":"1520-6882","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,28]]}}}