{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:00:44Z","timestamp":1791385244947,"version":"4.3.3"},"reference-count":42,"publisher":"American Chemical Society (ACS)","issue":"10","license":[{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-23-CE44-0041"],"award-info":[{"award-number":["ANR-23-CE44-0041"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010664","name":"H2020 Future and Emerging Technologies","doi-asserted-by":"publisher","award":["964553"],"award-info":[{"award-number":["964553"]}],"id":[{"id":"10.13039\/100010664","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Top-down (TD) Fourier transform mass spectrometry (FTMS) of proteins generates highly information-rich mass spectra. However, the resulting spectral complexity can hinder data interpretation and method applicability. Here, we apply transient-mediated, instrument-specific simulations of protein TD mass spectra with user-defined product ion identities. The workflow integrates sequence-based product ion generation, empirically informed fragmentation statistics, charge location modeling, and user-specified FT processing approach. The simulations capture key FTMS characteristics, including m\/z-dependent resolution, peak interference, and realistic peak shapes. As a proof of concept, we simulated carbonic anhydrase II TDMS data sets under conditions reported for corresponding 21 T ion cyclotron resonance (ICR) FTMS electron transfer dissociation experiments. The simulated mass spectra reproduced key experimental descriptors of spectral complexity, including peak density, spectral dynamic range, and isotopic structures. Using data sets with increasing complexity, we performed an initial evaluation of TDMS annotation performance and observed an expected decrease in product ion annotation rates from c-ion-only mass spectra to the most complex data sets containing a-, c-, y-, and z-type product ions, reflecting the impact of spectral congestion on confident assignment. These results demonstrate that realistic in silico TDMS data sets can support systematic investigation of spectral properties in TDMS and facilitate the development and evaluation of proteoform-specific data analysis approaches. The initial data set of simulated mass spectra and transients is available through ProteomeXchange under identifier PXD075270.<\/jats:p>","DOI":"10.1021\/jasms.6c00199","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T20:34:28Z","timestamp":1788467668000},"page":"2422-2431","source":"Crossref","is-referenced-by-count":0,"title":["<i>In Silico<\/i>\n                    Top-Down Fourier Transform\nMass Spectra to Advance Proteoform Analysis Methods"],"prefix":"10.1021","volume":"37","author":[{"given":"Nina A.","family":"Khristenko","sequence":"first","affiliation":[{"name":"Spectrotech , ,","place":["Lyon, France, 69006"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantin O.","family":"Nagornov","sequence":"additional","affiliation":[{"name":"Spectroswiss , ,","place":["Lausanne, Switzerland, 1015"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anton N.","family":"Kozhinov","sequence":"additional","affiliation":[{"name":"Spectroswiss , ,","place":["Lausanne, Switzerland, 1015"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David P. A.","family":"Kilgour","sequence":"additional","affiliation":[{"name":"Vibrat-Ion , , ,","place":["Aberystwyth, Wales, U.K., SY23 3AF"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7533-0774","authenticated-orcid":true,"given":"Yury O.","family":"Tsybin","sequence":"additional","affiliation":[{"name":"Spectrotech , ,","place":["Lyon, France, 69006"]},{"name":"Spectroswiss , ,","place":["Lausanne, Switzerland, 1015"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,3]]},"reference":[{"issue":"1","key":"2026100710064259700_cit1","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1038\/s43586-024-00318-2","article-title":"Top-down proteomics","volume":"4","author":"Roberts","year":"2024","journal-title":"Nat. Rev. Methods Primers"},{"issue":"18","key":"2026100710064259700_cit2","doi-asserted-by":"publisher","first-page":"12193","DOI":"10.1021\/acs.analchem.0c01064","article-title":"Increased\nsingle-spectrum top-down protein sequence coverage in trapping mass\nspectrometers with chimeric ion loading","volume":"92","author":"Weisbrod","year":"2020","journal-title":"Anal.\nChem."},{"issue":"7","key":"2026100710064259700_cit3","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/s41592-019-0457-0","article-title":"Best practices and benchmarks\nfor intact protein analysis for top-down\nmass spectrometry","volume":"16","author":"Donnelly","year":"2019","journal-title":"Nat. Methods"},{"issue":"7","key":"2026100710064259700_cit4","doi-asserted-by":"publisher","first-page":"100989","DOI":"10.1016\/j.mcpro.2025.100989","article-title":"Top-down and middle-down\nmass spectrometry of antibodies","volume":"24","author":"Khristenko","year":"2025","journal-title":"Mol. Cell.\nProteomics"},{"issue":"1\u20132","key":"2026100710064259700_cit5","doi-asserted-by":"publisher","first-page":"114","DOI":"10.2533\/chimia.2022.114","article-title":"Structural\nanalysis of monoclonal antibodies with top-down and middle-down electron\ntransfer dissociation mass spectrometry: the first decade","volume":"76","author":"Fornelli","year":"2022","journal-title":"Chimia"},{"issue":"6","key":"2026100710064259700_cit6","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1021\/jasms.1c00099","article-title":"Novel strategies to address the challenges in top-down\nproteomics","volume":"32","author":"Melby","year":"2021","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"12","key":"2026100710064259700_cit7","doi-asserted-by":"publisher","first-page":"2772","DOI":"10.1074\/mcp.M110.002766","article-title":"Deconvolution\nand database search of complex tandem mass spectra of intact proteins:\na combinatorial approach","volume":"9","author":"Liu","year":"2010","journal-title":"Mol. Cell. Proteomics"},{"issue":"2","key":"2026100710064259700_cit8","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1074\/mcp.O115.054387","article-title":"MASH Suite\nPro: A comprehensive software tool for top-down proteomics","volume":"15","author":"Cai","year":"2016","journal-title":"Mol. Cell. Proteomics"},{"issue":"7","key":"2026100710064259700_cit9","doi-asserted-by":"publisher","first-page":"1113","DOI":"10.1021\/jasms.1c00336","article-title":"Characterization\nof the time-domain isotopic beat patterns of monoclonal antibodies\nin Fourier transform mass spectrometry","volume":"33","author":"Nagornov","year":"2022","journal-title":"J. Am.\nSoc. Mass Spectrom."},{"issue":"8","key":"2026100710064259700_cit10","doi-asserted-by":"publisher","first-page":"4370","DOI":"10.1021\/acs.analchem.5b00140","article-title":"Bayesian deconvolution\nof mass and ion mobility spectra:\nfrom binary interactions to polydisperse ensembles","volume":"87","author":"Marty","year":"2015","journal-title":"Anal. Chem."},{"issue":"22","key":"2026100710064259700_cit11","doi-asserted-by":"publisher","first-page":"3495","DOI":"10.1093\/bioinformatics\/btw398","article-title":"TopPIC: a\nsoftware tool for top-down mass spectrometry-based\nproteoform identification and characterization","volume":"32","author":"Kou","year":"2016","journal-title":"Bioinformatics"},{"issue":"3","key":"2026100710064259700_cit12","doi-asserted-by":"publisher","first-page":"2079","DOI":"10.1021\/acs.analchem.8b04515","article-title":"Structural\nanalysis of monoclonal antibodies by ultrahigh resolution MALDI in-source\ndecay FT-ICR mass spectrometry","volume":"91","author":"van der Burgt","year":"2019","journal-title":"Anal. Chem."},{"issue":"2","key":"2026100710064259700_cit13","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/j.cels.2020.01.003","article-title":"FLASHDeconv: ultrafast, high-quality feature deconvolution\nfor top-down proteomics","volume":"10","author":"Jeong","year":"2020","journal-title":"Cell Syst."},{"key":"2026100710064259700_cit14","doi-asserted-by":"publisher","first-page":"gkaf740","DOI":"10.1093\/nar\/gkaf740","article-title":"Direct histone proteoform\nprofiling of the unannotated, endangered coral Acropora cervicornis","volume":"53","author":"Fuller","year":"2025","journal-title":"Nucleic Acids Res."},{"issue":"9","key":"2026100710064259700_cit15","doi-asserted-by":"publisher","first-page":"100814","DOI":"10.1016\/j.mcpro.2024.100814","article-title":"Are internal fragments observable in electron\nbased top-down mass spectrometry?","volume":"23","author":"Mikawy","year":"2024","journal-title":"Mol. Cell.\nProteomics"},{"issue":"13","key":"2026100710064259700_cit16","doi-asserted-by":"publisher","first-page":"2027","DOI":"10.1021\/ac951158i","article-title":"Ultrahigh-speed calculation of isotope distributions","volume":"68","author":"Rockwood","year":"1996","journal-title":"Anal. Chem."},{"issue":"5","key":"2026100710064259700_cit17","doi-asserted-by":"publisher","first-page":"1223","DOI":"10.1021\/ci300563h","article-title":"ChemCalc: a building\nblock for tomorrow\u2019s chemical infrastructure","volume":"53","author":"Patiny","year":"2013","journal-title":"J. Chem. Inf. Model."},{"issue":"1","key":"2026100710064259700_cit18","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1007\/s13361-013-0733-7","article-title":"Molecular\nIsotopic Distribution Analysis\n(MIDAs) with adjustable mass accuracy","volume":"25","author":"Alves","year":"2014","journal-title":"J. Am.\nSoc. Mass Spectrom."},{"issue":"11","key":"2026100710064259700_cit19","doi-asserted-by":"publisher","first-page":"5738","DOI":"10.1021\/acs.analchem.5b00941","article-title":"Accelerated isotope fine structure calculation using\npruned transition trees","volume":"87","author":"Loos","year":"2015","journal-title":"Anal. Chem."},{"issue":"6","key":"2026100710064259700_cit20","doi-asserted-by":"publisher","first-page":"3272","DOI":"10.1021\/acs.analchem.6b01459","article-title":"IsoSpec: hyperfast\nfine structure calculator","volume":"89","author":"Lacki","year":"2017","journal-title":"Anal. Chem."},{"issue":"9","key":"2026100710064259700_cit21","doi-asserted-by":"publisher","first-page":"1927","DOI":"10.1021\/jasms.0c00190","article-title":"Transient-mediated\nsimulations of FTMS isotopic distributions and mass spectra to guide\nexperiment design and data analysis","volume":"31","author":"Nagornov","year":"2020","journal-title":"J. Am.\nSoc. Mass Spectrom."},{"issue":"9","key":"2026100710064259700_cit22","doi-asserted-by":"publisher","first-page":"1787","DOI":"10.1007\/s13361-017-1702-3","article-title":"Front-end electron transfer dissociation coupled\nto a 21 T FT-ICR mass spectrometer for intact protein sequence analysis","volume":"28","author":"Weisbrod","year":"2017","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"6","key":"2026100710064259700_cit23","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1007\/s13361-017-1635-x","article-title":"Defining\ngas-phase fragmentation propensities of intact proteins during native\ntop-down mass spectrometry","volume":"28","author":"Haverland","year":"2017","journal-title":"J. Am. Soc. Mass\nSpectrom."},{"issue":"32","key":"2026100710064259700_cit24","doi-asserted-by":"publisher","first-page":"5301","DOI":"10.1002\/anie.200601240","article-title":"Complementary\nsequence\npreferences of electron-capture dissociation and vibrational excitation\nin fragmentation of polypeptide polycations","volume":"45","author":"Savitski","year":"2006","journal-title":"Angew. Chem., Int. Ed."},{"issue":"12","key":"2026100710064259700_cit25","doi-asserted-by":"publisher","first-page":"2273","DOI":"10.1016\/j.jasms.2009.08.019","article-title":"Electron capture dissociation product\nion abundances at the X amino acid in RAAAA-X-AAAAK peptides correlate\nwith amino acid polarity and radical stability","volume":"20","author":"Vorobyev","year":"2009","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"43","key":"2026100710064259700_cit26","doi-asserted-by":"publisher","first-page":"13911","DOI":"10.1021\/jp107450n","article-title":"Accurate proton\naffinity and gas-phase\nbasicity values for molecules important in biocatalysis","volume":"114","author":"Moser","year":"2010","journal-title":"J. Phys. Chem. B"},{"issue":"12","key":"2026100710064259700_cit27","doi-asserted-by":"publisher","first-page":"3465","DOI":"10.1074\/mcp.M113.030114","article-title":"Large-scale top-down\nproteomics of the human proteome: membrane proteins, mitochondria,\nand senescence","volume":"12","author":"Catherman","year":"2013","journal-title":"Mol. Cell. Proteomics"},{"issue":"23","key":"2026100710064259700_cit28","doi-asserted-by":"publisher","first-page":"8919","DOI":"10.1021\/ac201293m","article-title":"Structural Analysis\nof Intact Monoclonal Antibodies by Electron Transfer Dissociation\nMass Spectrometry","volume":"83","author":"Tsybin","year":"2011","journal-title":"Anal. Chem."},{"key":"2026100710064259700_cit29","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1016\/j.jprot.2017.02.013","article-title":"Top-down\nanalysis of immunoglobulin G isotypes 1 and 2 with electron transfer\ndissociation on a high-field Orbitrap mass spectrometer","volume":"159","author":"Fornelli","year":"2017","journal-title":"J. Proteomics"},{"key":"2026100710064259700_cit30","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi1318s37","article-title":"Identification\nof peptide features in precursor spectra using Hardklor and Kronik","volume-title":"Current Protocols in Bioinformatics","author":"Hoopmann","year":"2012"},{"issue":"13","key":"2026100710064259700_cit31","doi-asserted-by":"publisher","first-page":"6437","DOI":"10.1021\/ac400972y","article-title":"Iterative\nmethod for mass spectra\nrecalibration via empirical estimation of the mass calibration function\nfor Fourier transform mass spectrometry-based petroleomics","volume":"85","author":"Kozhinov","year":"2013","journal-title":"Anal. Chem."},{"issue":"12","key":"2026100710064259700_cit32","doi-asserted-by":"publisher","first-page":"2647","DOI":"10.1021\/jasms.5c00256","article-title":"Top-down\nmass spectrometry of a clinical antibody\nlight chain using the omnitrap-orbitrap-booster platform","volume":"36","author":"Garcia","year":"2025","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"2","key":"2026100710064259700_cit33","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1007\/s13361-016-1549-z","article-title":"Autopiquer - a robust\nand reliable peak detection algorithm\nfor mass spectrometry","volume":"28","author":"Kilgour","year":"2017","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"3","key":"2026100710064259700_cit34","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/S1044-0305(00)00223-3","article-title":"Electron\ncapture dissociation of gaseous multiply charged ions by Fourier-transform\nion cyclotron resonance","volume":"12","author":"McLafferty","year":"2001","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"12","key":"2026100710064259700_cit35","doi-asserted-by":"publisher","first-page":"5014","DOI":"10.1039\/c3cs35477f","article-title":"Principles\nof electron capture and transfer dissociation mass spectrometry applied\nto peptide and protein structure analysis","volume":"42","author":"Zhurov","year":"2013","journal-title":"Chem.\nSoc. Rev."},{"issue":"17","key":"2026100710064259700_cit36","doi-asserted-by":"publisher","first-page":"6868","DOI":"10.1021\/ac2010795","article-title":"On the scalability\nand requirements of whole protein mass spectrometry","volume":"83","author":"Compton","year":"2011","journal-title":"Anal. Chem."},{"issue":"1","key":"2026100710064259700_cit37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/(SICI)1098-2787(1998)17:1&lt;1:AID-MAS1&gt;3.0.CO;2-K","article-title":"Fourier transform ion cyclotron resonance\nmass spectrometry: a primer","volume":"17","author":"Marshall","year":"1998","journal-title":"Mass Spectrom.\nRev."},{"key":"2026100710064259700_cit38","doi-asserted-by":"crossref","DOI":"10.1016\/B978-0-12-814013-0.00005-3","article-title":"Advanced fundamentals\nin Fourier transform mass spectrometry","volume-title":"Fundamentals and Applications of Fourier Transform Mass Spectrometry","author":"Tsybin","year":"2019"},{"issue":"5","key":"2026100710064259700_cit39","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1002\/mas.21414","article-title":"Data processing in Fourier transform\nion cyclotron\nresonance mass spectrometry","volume":"33","author":"Qi","year":"2014","journal-title":"Mass Spectrom.\nRev."},{"key":"2026100710064259700_cit40","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1016\/j.ijms.2014.05.019","article-title":"Enhanced Fourier transform\nfor Orbitrap mass spectrometry","volume":"369","author":"Lange","year":"2014","journal-title":"Int. J. Mass\nSpectrom."},{"issue":"8","key":"2026100710064259700_cit41","doi-asserted-by":"publisher","first-page":"3903","DOI":"10.1021\/ac303289c","article-title":"Autophaser:\nan algorithm for automated generation of absorption mode spectra for\nFT-ICR MS","volume":"85","author":"Kilgour","year":"2013","journal-title":"Anal. Chem."},{"issue":"D1","key":"2026100710064259700_cit42","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkae1011","article-title":"The PRIDE database at\n20 years: 2025 update","volume":"53","author":"Perez-Riverol","year":"2025","journal-title":"Nucleic Acids Res."}],"container-title":["Journal of the American\nSociety for Mass Spectrometry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/jasms.6c00199","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jamsef\/article-pdf\/37\/10\/2422\/68281831\/jasms.6c00199.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jamsef\/article-pdf\/37\/10\/2422\/68281831\/jasms.6c00199.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T14:31:51Z","timestamp":1791383511000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jamsef\/article\/37\/10\/2422\/5412908\/In-Silico-Top-Down-Fourier-Transform-Mass-Spectra"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,3]]},"references-count":42,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,9,3]]},"published-print":{"date-parts":[[2026,10,7]]}},"URL":"https:\/\/doi.org\/10.1021\/jasms.6c00199","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv.15003684\/v1","asserted-by":"object"},{"id-type":"doi","id":"10.26434\/chemrxiv.15003684\/v2","asserted-by":"object"}]},"ISSN":["1044-0305","1879-1123"],"issn-type":[{"value":"1044-0305","type":"print"},{"value":"1879-1123","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,3]]}}}