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Compared to genetic variations, changes in the molecular structure and state of a protein (i.e. proteoforms) are more directly related to pathological changes in diseases. Characterizing proteoforms involves identifying and locating primary structure alterations (PSAs) in proteoforms, which is of practical importance for the advancement of the medical profession. With the development of mass spectrometry (MS) technology, the characterization of proteoforms based on top-down MS technology has become possible. This type of method is relatively new and faces many challenges. Since the proteoform identification is the most important process in characterizing proteoforms, we comprehensively review the existing proteoform identification methods in this study. Before identifying proteoforms, the spectra need to be preprocessed, and protein sequence databases can be filtered to speed up the identification. Therefore, we also summarize some popular deconvolution algorithms, various filtering algorithms for improving the proteoform identification performance and various scoring methods for localizing proteoforms. Moreover, commonly used methods were evaluated and compared in this review. We believe our review could help researchers better understand the current state of the development in this field and design new efficient algorithms for the proteoform characterization.<\/jats:p>","DOI":"10.1093\/bib\/bbaa015","type":"journal-article","created":{"date-parts":[[2020,2,15]],"date-time":"2020-02-15T12:11:50Z","timestamp":1581768710000},"page":"1729-1750","source":"Crossref","is-referenced-by-count":7,"title":["Proteoform characterization based on top-down mass spectrometry"],"prefix":"10.1093","volume":"22","author":[{"given":"Jiancheng","family":"Zhong","sequence":"first","affiliation":[{"name":"College of Information Science and Engineering, Hunan Normal University, Changsha, Hunan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yusui","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Information Science and Engineering, Hunan Normal University, Changsha, Hunan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minzhu","family":"Xie","sequence":"additional","affiliation":[{"name":"College of Information Science and Engineering, Hunan Normal University, Changsha, Hunan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Peng","sequence":"additional","affiliation":[{"name":"Kunming University of Science and Technology, Kunming, Yunnan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chushu","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Information Science and Engineering, Hunan Normal University, Changsha, Hunan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4593-9332","authenticated-orcid":false,"given":"Fang-Xiang","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Engineering and the Department of Computer Science at University of Saskatchewan, Saskatoon, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianxin","family":"Wang","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering at Central South University, Changsha, Hunan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,3,2]]},"reference":[{"key":"2021032314281406500_ref1","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1074\/jbc.M111.293258","article-title":"Augmented phosphorylation of cardiac troponin i in hypertensive heart failure","volume":"287","author":"Dong","year":"2012","journal-title":"J Biol Chem"},{"key":"2021032314281406500_ref2","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1126\/science.1186088","article-title":"Altered histone acetylation is associated with age-dependent memory impairment in mice","volume":"328","author":"Peleg","year":"2010","journal-title":"Science"},{"key":"2021032314281406500_ref3","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/nmeth.2369","article-title":"Consortium for top down proteomics. 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