{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T03:17:42Z","timestamp":1785208662328,"version":"3.55.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,6,9]],"date-time":"2023-06-09T00:00:00Z","timestamp":1686268800000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM125085"],"award-info":[{"award-number":["R01 GM125085"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Native top-down proteomics (nTDP) integrates native mass spectrometry (nMS) with top-down proteomics (TDP) to provide comprehensive analysis of protein complexes together with proteoform identification and characterization. Despite significant advances in nMS and TDP software developments, a unified and user-friendly software package for analysis of nTDP data remains lacking.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed MASH Native to provide a unified solution for nTDP to process complex datasets with database searching capabilities in a user-friendly interface. MASH Native supports various data formats and incorporates multiple options for deconvolution, database searching, and spectral summing to provide a \u201cone-stop shop\u201d for characterizing both native protein complexes and proteoforms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The MASH Native app, video tutorials, written tutorials, and additional documentation are freely available for download at https:\/\/labs.wisc.edu\/gelab\/MASH_Explorer\/MASHSoftware.php. All data files shown in user tutorials are included with the MASH Native software in the download .zip file.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad359","type":"journal-article","created":{"date-parts":[[2023,6,9]],"date-time":"2023-06-09T14:04:53Z","timestamp":1686319493000},"source":"Crossref","is-referenced-by-count":36,"title":["MASH Native: a unified solution for native top-down proteomics data processing"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1354-0722","authenticated-orcid":false,"given":"Eli J","family":"Larson","sequence":"first","affiliation":[{"name":"Department of Chemistry, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa R","family":"Pergande","sequence":"additional","affiliation":[{"name":"Department of Cell and Regenerative Biology, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle E","family":"Moss","sequence":"additional","affiliation":[{"name":"Department of Cell and Regenerative Biology, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kalina J","family":"Rossler","sequence":"additional","affiliation":[{"name":"Department of Cell and Regenerative Biology, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R Kent","family":"Wenger","sequence":"additional","affiliation":[{"name":"Department of Cell and Regenerative Biology, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"},{"name":"Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boris","family":"Krichel","sequence":"additional","affiliation":[{"name":"Department of Cell and Regenerative Biology, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harini","family":"Josyer","sequence":"additional","affiliation":[{"name":"Department of Cell and Regenerative Biology, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jake A","family":"Melby","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0478-4987","authenticated-orcid":false,"given":"David S","family":"Roberts","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyndalanne","family":"Pike","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuoxin","family":"Shi","sequence":"additional","affiliation":[{"name":"Department of Cell and Regenerative Biology, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsin-Ju","family":"Chan","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bridget","family":"Knight","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Holden T","family":"Rogers","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyle A","family":"Brown","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irene M","family":"Ong","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"},{"name":"University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison , Madison, WI 53705, United States"},{"name":"Department of Obstetrics and Gynecology, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyowon","family":"Jeong","sequence":"additional","affiliation":[{"name":"Department of Applied Bioinformatics, University of T\u00fcbingen , T\u00fcbingen 72704, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael T","family":"Marty","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of Arizona , Tucson, AZ 85719, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean J","family":"McIlwain","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"},{"name":"University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Ge","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"},{"name":"Department of Cell and Regenerative Biology, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"},{"name":"Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin\u2013Madison , Madison, WI 53705, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,6,9]]},"reference":[{"key":"2023062111033039700_btad359-B1","doi-asserted-by":"crossref","first-page":"7778","DOI":"10.1021\/acs.analchem.0c00903","article-title":"EnvCNN: a convolutional neural network model for evaluating isotopic envelopes in top-down mass-spectral deconvolution","volume":"92","author":"Basharat","year":"2020","journal-title":"Anal Chem"},{"key":"2023062111033039700_btad359-B2","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1074\/mcp.O115.054387","article-title":"MASH suite pro: a comprehensive software tool for top-down proteomics","volume":"15","author":"Cai","year":"2016","journal-title":"Mol Cell Proteomics"},{"key":"2023062111033039700_btad359-B3","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1016\/j.bbrc.2014.02.041","article-title":"Top down proteomics: facts and perspectives","volume":"445","author":"Catherman","year":"2014","journal-title":"Biochem Biophys Res Commun"},{"key":"2023062111033039700_btad359-B4","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/nbt.2377","article-title":"A cross-platform toolkit for mass spectrometry and proteomics","volume":"30","author":"Chambers","year":"2012","journal-title":"Nat Biotechnol"},{"key":"2023062111033039700_btad359-B5","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1021\/acs.analchem.7b04747","article-title":"Top-down proteomics: ready for prime time?","volume":"90","author":"Chen","year":"2018","journal-title":"Anal Chem"},{"key":"2023062111033039700_btad359-B6","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1007\/s13361-018-2018-7","article-title":"Extracting charge and mass information from highly congested mass spectra using Fourier-domain harmonics","volume":"29","author":"Cleary","year":"2018","journal-title":"J Am Soc Mass Spectrom"},{"key":"2023062111033039700_btad359-B7","doi-asserted-by":"crossref","first-page":"6205","DOI":"10.1021\/acs.analchem.6b01088","article-title":"Fourier analysis method for analyzing highly congested mass spectra of ion populations with repeated subunits","volume":"88","author":"Cleary","year":"2016","journal-title":"Anal Chem"},{"key":"2023062111033039700_btad359-B8","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1002\/pmic.201400313","article-title":"ProSight lite: graphical software to analyze top-down mass spectrometry data","volume":"15","author":"Fellers","year":"2015","journal-title":"Proteomics"},{"key":"2023062111033039700_btad359-B9","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1002\/rcm.1290050810","article-title":"Maximum entropy deconvolution in electrospray mass spectrometry","volume":"5","author":"Ferrige","year":"1991","journal-title":"Rapid Commun Mass Spectrom"},{"key":"2023062111033039700_btad359-B10","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/S1044-0305(99)00157-9","article-title":"Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules","volume":"11","author":"Horn","year":"2000","journal-title":"J Am Soc Mass Spectrom"},{"key":"2023062111033039700_btad359-B11","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.cels.2020.01.003","article-title":"FLASHDeconv: ultrafast, high-quality feature deconvolution for top-down proteomics","volume":"10","author":"Jeong","year":"2020","journal-title":"Cell Syst"},{"key":"2023062111033039700_btad359-B12","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1021\/acs.accounts.2c00216","article-title":"Native mass spectrometry at the convergence of structural biology and compositional proteomics","volume":"55","author":"Joo\u00df","year":"2022","journal-title":"Acc Chem Res"},{"key":"2023062111033039700_btad359-B13","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1146\/annurev-biophys-092721-085421","article-title":"Native mass spectrometry: recent progress and remaining challenges","volume":"51","author":"Karch","year":"2022","journal-title":"Annu Rev Biophys"},{"key":"2023062111033039700_btad359-B14","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1021\/acs.analchem.0c04342","article-title":"Native mass spectrometry of membrane proteins","volume":"93","author":"Keener","year":"2021","journal-title":"Anal Chem"},{"key":"2023062111033039700_btad359-B15","doi-asserted-by":"crossref","first-page":"3495","DOI":"10.1093\/bioinformatics\/btw398","article-title":"TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization","volume":"32","author":"Kou","year":"2016","journal-title":"Bioinformatics"},{"key":"2023062111033039700_btad359-B16","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1021\/acs.jproteome.0c00952","article-title":"ClipsMS: an algorithm for analyzing internal fragments resulting from top-down mass spectrometry","volume":"20","author":"Lantz","year":"2021","journal-title":"J Proteome Res"},{"key":"2023062111033039700_btad359-B17","first-page":"21826","author":"Lantz"},{"key":"2023062111033039700_btad359-B18","doi-asserted-by":"crossref","first-page":"10013","DOI":"10.1021\/acs.analchem.1c00150","article-title":"High-throughput multi-attribute analysis of antibody-drug conjugates enabled by trapped ion mobility spectrometry and top-down mass spectrometry","volume":"93","author":"Larson","year":"2021","journal-title":"Anal Chem"},{"key":"2023062111033039700_btad359-B19","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s13361-016-1545-3","article-title":"Native mass spectrometry: what is in the name?","volume":"28","author":"Leney","year":"2017","journal-title":"J Am Soc Mass Spectrom"},{"key":"2023062111033039700_btad359-B20","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1038\/nchem.2908","article-title":"An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes","volume":"10","author":"Li","year":"2018","journal-title":"Nat Chem"},{"key":"2023062111033039700_btad359-B21","first-page":"1","article-title":"Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes","author":"Liu","year":"2022","journal-title":"Mass Spectrom. Rev"},{"key":"2023062111033039700_btad359-B22","doi-asserted-by":"crossref","first-page":"2772","DOI":"10.1074\/mcp.M110.002766","article-title":"Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach","volume":"9","author":"Liu","year":"2010","journal-title":"Mol Cell Proteomics"},{"key":"2023062111033039700_btad359-B23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1074\/mcp.M111.008524","article-title":"Protein identification using top-down","volume":"11","author":"Liu","year":"2012","journal-title":"Mol Cell Proteomics"},{"key":"2023062111033039700_btad359-B24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/(SICI)1098-2787(1997)16:1<1::AID-MAS1>3.0.CO;2-L","article-title":"Studying noncovalent protein complexes by electrospray ionization mass spectrometry","volume":"16","author":"Loo","year":"1997","journal-title":"Mass Spectrom Rev"},{"key":"2023062111033039700_btad359-B25","doi-asserted-by":"crossref","first-page":"4370","DOI":"10.1021\/acs.analchem.5b00140","article-title":"Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles","volume":"87","author":"Marty","year":"2015","journal-title":"Anal Chem"},{"key":"2023062111033039700_btad359-B26","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1021\/jasms.0c00035","article-title":"Enhancing top-down proteomics data analysis by combining deconvolution results through a machine learning strategy","volume":"31","author":"Mcilwain","year":"2020","journal-title":"J. Am. Soc. Mass Spectrom"},{"key":"2023062111033039700_btad359-B27","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1021\/jasms.1c00099","article-title":"Novel strategies to address the challenges in top-down proteomics","volume":"32","author":"Melby","year":"2021","journal-title":"J Am Soc Mass Spectrom"},{"key":"2023062111033039700_btad359-B28","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1038\/nmeth.4388","article-title":"Informed-proteomics: open-source software package for top-down proteomics","volume":"14","author":"Park","year":"2017","journal-title":"Nat Methods"},{"key":"2023062111033039700_btad359-B29","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1007\/s13361-018-1951-9","article-title":"MetaUniDec: high-throughput deconvolution of native mass spectra MS data set MetaUniDec deconvolution integration & extraction","volume":"30","author":"Reid","year":"2019","journal-title":"J Am Soc Mass Spectrom"},{"key":"2023062111033039700_btad359-B30","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1146\/annurev.biochem.76.061005.090816","article-title":"The role of mass spectrometry in structure elucidation of dynamic protein complexes","volume":"76","author":"Sharon","year":"2007","journal-title":"Annu Rev Biochem"},{"key":"2023062111033039700_btad359-B31","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/nchembio.2515","article-title":"Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes","volume":"14","author":"Skinner","year":"2018","journal-title":"Nat Chem Biol"},{"key":"2023062111033039700_btad359-B32","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/nchembio.2515","article-title":"Top-down characterization of endogenous protein complexes with native proteomics","volume":"14","author":"Skinner","year":"2018","journal-title":"Nat Chem Biol"},{"key":"2023062111033039700_btad359-B33","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1021\/acs.analchem.8b05071","article-title":"Surface-induced dissociation: an effective method for characterization of protein quaternary structure","volume":"91","author":"Stiving","year":"2019","journal-title":"Anal Chem"},{"key":"2023062111033039700_btad359-B34","doi-asserted-by":"crossref","first-page":"3082","DOI":"10.1021\/acs.analchem.5b03963","article-title":"pTop 1.0: a high-accuracy and high-efficiency search engine for intact protein identification","volume":"88","author":"Sun","year":"2016","journal-title":"Anal Chem"},{"key":"2023062111033039700_btad359-B35","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1146\/annurev-anchem-071015-041550","article-title":"Progress in top-down proteomics and the analysis of proteoforms","volume":"9","author":"Toby","year":"2016","journal-title":"Annu Rev Anal Chem (Palo Alto Calif)"},{"key":"2023062111033039700_btad359-B36","doi-asserted-by":"crossref","first-page":"3867","DOI":"10.1021\/acs.jproteome.0c00469","article-title":"MASH explorer: a universal software environment for top-down proteomics","volume":"19","author":"Wu","year":"2020","journal-title":"J Proteome Res"},{"key":"2023062111033039700_btad359-B37","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1002\/pmic.201100081","article-title":"pParse: a method for accurate determination of monoisotopic peaks in high-resolution mass spectra","volume":"12","author":"Yuan","year":"2012","journal-title":"Proteomics"},{"key":"2023062111033039700_btad359-B38","doi-asserted-by":"crossref","first-page":"12918","DOI":"10.1039\/D0SC04392C","article-title":"Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry","volume":"11","author":"Zhou","year":"2020","journal-title":"Chem Sci"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad359\/50563059\/btad359.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/6\/btad359\/50664577\/btad359.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/6\/btad359\/50664577\/btad359.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,21]],"date-time":"2023-06-21T07:26:01Z","timestamp":1687332361000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad359\/7192985"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,6,1]]},"references-count":38,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad359","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.01.02.522513","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,6,1]]},"published":{"date-parts":[[2023,6,1]]},"article-number":"btad359"}}