{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T16:28:23Z","timestamp":1775924903158,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,9,29]],"date-time":"2021-09-29T00:00:00Z","timestamp":1632873600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Max-Planck Society for Advancement of Science and by the Bavarian State Ministry of Health and Care"},{"name":"Postdoc.Mobility fellowship granted by the Swiss National Science Foundation","award":["P400PB_191046"],"award-info":[{"award-number":["P400PB_191046"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Integrating experimental information across proteomic datasets with the wealth of publicly available sequence annotations is a crucial part in many proteomic studies that currently lacks an automated analysis platform. Here, we present AlphaMap, a Python package that facilitates the visual exploration of peptide-level proteomics data. Identified peptides and post-translational modifications in proteomic datasets are mapped to their corresponding protein sequence and visualized together with prior knowledge from UniProt and with expected proteolytic cleavage sites. The functionality of AlphaMap can be accessed via an intuitive graphical user interface or\u2014more flexibly\u2014as a Python package that allows its integration into common analysis workflows for data visualization. AlphaMap produces publication-quality illustrations and can easily be customized to address a given research question.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>AlphaMap is implemented in Python and released under an Apache license. The source code and one-click installers are freely available at https:\/\/github.com\/MannLabs\/alphamap.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab674","type":"journal-article","created":{"date-parts":[[2021,9,22]],"date-time":"2021-09-22T23:15:06Z","timestamp":1632352506000},"page":"849-852","source":"Crossref","is-referenced-by-count":18,"title":["AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge"],"prefix":"10.1093","volume":"38","author":[{"given":"Eugenia","family":"Voytik","sequence":"first","affiliation":[{"name":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , 82152 Martinsried, Germany"}]},{"given":"Isabell","family":"Bludau","sequence":"additional","affiliation":[{"name":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , 82152 Martinsried, Germany"}]},{"given":"Sander","family":"Willems","sequence":"additional","affiliation":[{"name":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , 82152 Martinsried, Germany"}]},{"given":"Fynn M","family":"Hansen","sequence":"additional","affiliation":[{"name":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , 82152 Martinsried, Germany"}]},{"given":"Andreas-David","family":"Brunner","sequence":"additional","affiliation":[{"name":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , 82152 Martinsried, Germany"}]},{"given":"Maximilian T","family":"Strauss","sequence":"additional","affiliation":[{"name":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , 82152 Martinsried, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1292-4799","authenticated-orcid":false,"given":"Matthias","family":"Mann","sequence":"additional","affiliation":[{"name":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , 82152 Martinsried, Germany"},{"name":"Department of Clinical Proteomics, NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2021,9,29]]},"reference":[{"key":"2023020108484985100_btab674-B1","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1038\/nature01511","article-title":"Mass spectrometry-based proteomics","volume":"422","author":"Aebersold","year":"2003","journal-title":"Nature"},{"key":"2023020108484985100_btab674-B2","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nature19949","article-title":"Mass-spectrometric exploration of proteome structure and function","volume":"537","author":"Aebersold","year":"2016","journal-title":"Nature"},{"key":"2023020108484985100_btab674-B3","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"Bateman","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023020108484985100_btab674-B4","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"In Nucleic Acids Res"},{"key":"2023020108484985100_btab674-B5","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1074\/mcp.M114.044305","article-title":"Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues","volume":"14","author":"Bruderer","year":"2015","journal-title":"Mol. 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