{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,2]],"date-time":"2022-04-02T00:47:45Z","timestamp":1648860465222},"reference-count":14,"publisher":"Springer Science and Business Media LLC","issue":"S6","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures. Visualization of large data sets produced from LC-MS, namely the chromatogram and the mass spectra that correspond to its compounds is the focus of this work.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The in-house developed 'Brukin2D' software, built in Matlab 7.4, which is presented here, uses the compound data that are exported from the Bruker 'DataAnalysis' program, and depicts the mean mass spectra of all the chromatogram compounds from one LC-MS run, in one 2D contour\/density plot. Two contour plots from different chromatograph runs can then be viewed in the same window and automatically compared, in order to find their similarities and differences. The results of the comparison can be examined through detailed mass quantification tables, while chromatogram compound statistics are also calculated during the procedure.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>'Brukin2D' provides a user-friendly platform for quick, easy and integrated view of complex LC-MS data. The software is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.bioacademy.gr\/bioinformatics\/Brukin2d\/index.html\" ext-link-type=\"uri\">http:\/\/www.bioacademy.gr\/bioinformatics\/Brukin2d\/index.html<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-s6-s12","type":"journal-article","created":{"date-parts":[[2009,6,16]],"date-time":"2009-06-16T18:15:46Z","timestamp":1245176146000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["'Brukin2D': a 2D visualization and comparison tool for LC-MS data"],"prefix":"10.1186","volume":"10","author":[{"given":"Dimosthenis","family":"Tsagkrasoulis","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Panagiotis","family":"Zerefos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Loudos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonia","family":"Vlahou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Baumann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sophia","family":"Kossida","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,6,16]]},"reference":[{"key":"3307_CR1","doi-asserted-by":"publisher","DOI":"10.1385\/1592591302","volume-title":"Introduction to proteomics: Tools for the new biology","author":"DC Liebler","year":"2001","unstructured":"Liebler DC: Introduction to proteomics: Tools for the new biology. Humana Press; 2001."},{"key":"3307_CR2","doi-asserted-by":"publisher","first-page":"3856","DOI":"10.1021\/ac035375s","volume":"76","author":"X Li","year":"2004","unstructured":"Li X, Pedrioli PGA, Eng J, Martin D, Yi EC, Lee H, Aebersold R: A Tool To Visualize and Evaluate Data Obtained by Liquid Chromatography-Electrospray Ionization-Mass Spectrometry. Anal Chem 2004, 76: 3856\u20133860.","journal-title":"Anal Chem"},{"key":"3307_CR3","doi-asserted-by":"publisher","DOI":"10.1385\/1592591698","volume-title":"The Protein Protocols Handbook","author":"JM Walker","year":"2002","unstructured":"Walker JM: The Protein Protocols Handbook. Humana Press; 2002."},{"key":"3307_CR4","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1038\/nature01511","volume":"422","author":"R Aebersold","year":"2003","unstructured":"Aebersold R, Mann M: Mass spectrometry-based proteomics. Nature 2003, 422: 198\u2013207.","journal-title":"Nature"},{"key":"3307_CR5","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/10890","volume":"17","author":"AJ Link","year":"1999","unstructured":"Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR: Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 1999, 17: 676\u2013682.","journal-title":"Nat Biotechnol"},{"key":"3307_CR6","unstructured":"Brukin2D webpage[http:\/\/www.bioacademy.gr\/bioinformatics\/Brukin2d\/index.html]"},{"key":"3307_CR7","unstructured":"Software: Pep3D \u2013 SPCTools[http:\/\/tools.proteomecenter.org\/Pep3D.php]"},{"key":"3307_CR8","unstructured":"MSight[http:\/\/www.expasy.ch\/MSight\/]"},{"key":"3307_CR9","unstructured":"GeneBio: Phenyx[http:\/\/www.genebio.com\/products\/phenyx\/]"},{"issue":"9","key":"3307_CR10","doi-asserted-by":"publisher","first-page":"2381","DOI":"10.1002\/pmic.200401244","volume":"5","author":"PM Palagi","year":"2005","unstructured":"Palagi PM, Walther D, Quadroni M, Catherinet S, Burgess J, Zimmermann-Ivol CG, Sanchez JC, Binz PA, Hochstrasser DF, Appel RD: MSight: An image analysis software for liquid chromatography-mass spectrometry. Proteomics 2005, 5(9):2381\u20132384.","journal-title":"Proteomics"},{"key":"3307_CR11","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1007\/978-1-59745-117-8_19","volume":"428","author":"M Fitzgibbon","year":"2008","unstructured":"Fitzgibbon M, Law W, May D, Detter A, McIntosh M: Open-Source Platform for the Analysis of Liquid Chromatography-Mass Spectrometry (LC-MS) Data. Methods Mol Biol 2008, 428: 369\u2013382.","journal-title":"Methods Mol Biol"},{"key":"3307_CR12","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1186\/1471-2105-6-179","volume":"6","author":"M Katajamaa","year":"2005","unstructured":"Katajamaa M, Oresic M: Processing methods for differential analysis of LC\/MS profile data. BMC Bioinformatics 2005, 6: 179.","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"3307_CR13","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1093\/bioinformatics\/btk039","volume":"22","author":"M Katajamaa","year":"2006","unstructured":"Katajamaa M, Miettinen J, Oresic M: MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 2006, 22(5):634\u2013636.","journal-title":"Bioinformatics"},{"issue":"2","key":"3307_CR14","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1093\/bib\/bbn007","volume":"9","author":"P Veltri","year":"2008","unstructured":"Veltri P: Algorithms and tools for analysis and management of mass spectrometry data. Brief Bioinform 2008, 9(2):144\u2013155.","journal-title":"Brief Bioinform"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S6-S12.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T21:54:22Z","timestamp":1630446862000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-S6-S12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,6,16]]},"references-count":14,"journal-issue":{"issue":"S6","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["3307"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-s6-s12","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,6,16]]},"assertion":[{"value":"16 June 2009","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S12"}}