{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T03:50:37Z","timestamp":1782273037709,"version":"3.54.5"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,9,28]],"date-time":"2019-09-28T00:00:00Z","timestamp":1569628800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Federal Ministry for Education and Research","award":["03Z22HN22"],"award-info":[{"award-number":["03Z22HN22"]}]},{"name":"European Regional Development Funds","award":["ZS\/2016\/04\/78115"],"award-info":[{"award-number":["ZS\/2016\/04\/78115"]}]},{"DOI":"10.13039\/501100004350","name":"Studienstiftung des deutschen Volkes","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004350","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>A variety of search engines exists for the identification of peptide spectrum matches after cross-linking mass spectrometry experiments. The resulting diversity in output formats complicates data validation and visualization as well as exchange with collaborators, particularly from other research areas.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present CroCo, a user-friendly standalone executable to convert cross-linking results to a comprehensive spreadsheet format. Using this format, CroCo can be employed to generate input files for a selection of the commonly utilized validation and visualization tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source-code is freely available under a GNU general public license at https:\/\/github.com\/cschmidtlab\/croco. The standalone executable is available and documented at https:\/\/cschmidtlab.github.io\/CroCo.<\/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\/btz732","type":"journal-article","created":{"date-parts":[[2019,9,26]],"date-time":"2019-09-26T11:28:48Z","timestamp":1569497328000},"page":"1296-1297","source":"Crossref","is-referenced-by-count":10,"title":["The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3316-9999","authenticated-orcid":false,"given":"Julian","family":"Bender","sequence":"first","affiliation":[{"name":"Martin Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Interdisciplinary Research Center HALOmem , Charles Tanford Protein Center, 06120 Halle (Saale), Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9410-1424","authenticated-orcid":false,"given":"Carla","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Martin Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Interdisciplinary Research Center HALOmem , Charles Tanford Protein Center, 06120 Halle (Saale), Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,9,28]]},"reference":[{"key":"2023013110125341900_btz732-B1","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1074\/mcp.O114.042259","article-title":"xiNET: cross-link network maps with residue resolution","volume":"14","author":"Combe","year":"2015","journal-title":"Mol. Cell. Proteomics"},{"key":"2023013110125341900_btz732-B2","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1016\/j.str.2017.08.015","article-title":"Accommodating protein dynamics in the modeling of chemical crosslinks","volume":"25","author":"Degiacomi","year":"2017","journal-title":"Structure"},{"key":"2023013110125341900_btz732-B3","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1007\/s13361-011-0261-2","article-title":"StavroX\u2013a software for analyzing crosslinked products in protein interaction studies","volume":"23","author":"Gotze","year":"2012","journal-title":"J. Am. Soc. Mass Spectrom"},{"key":"2023013110125341900_btz732-B4","doi-asserted-by":"crossref","first-page":"W362","DOI":"10.1093\/nar\/gkv463","article-title":"xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints","volume":"43","author":"Grimm","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023013110125341900_btz732-B5","doi-asserted-by":"crossref","DOI":"10.3791\/56747-v","article-title":"Combining chemical cross-linking and mass spectrometry of intact protein complexes to study the architecture of multi-subunit protein assemblies","author":"Haupt","year":"2017","journal-title":"J. Vis. Exp."},{"key":"2023013110125341900_btz732-B6","doi-asserted-by":"crossref","first-page":"2190","DOI":"10.1021\/pr501321h","article-title":"Kojak: efficient analysis of chemically cross-linked protein complexes","volume":"14","author":"Hoopmann","year":"2015","journal-title":"J. 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