{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:05:55Z","timestamp":1761059155475},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Detection of protein spots in two-dimensional gel electrophoresis images (2-DE) is a very complex task and current approaches addressing this problem still suffer from significant shortcomings. When quantifying a spot, most of the current software applications include a lot of background due to poor segmentation. Other software applications use a fixed window for this task, resulting in omission of part of the protein spot, or including background in the quantification. The approach presented here for the segmentation and quantification of 2-DE aims to minimize these problems.<\/jats:p>\n               <jats:p>Results: Five sections from different gels are used to test the performance of the presented method concerning the detection of protein spots, and three gel sections are used to test the quantification of sixty protein spots. Comparisons with a state-of-the-art commercial software and an academic state-of-the-art approach are presented. It is shown that the proposed approach for segmentation and quantification of 2-DE images can compete with the available commercial and academic software packages.<\/jats:p>\n               <jats:p>Availability: A command-line prototype may be downloaded, for non-commercial use, from http:\/\/w3.ualg.pt\/~aanjos\/prototypes.html.<\/jats:p>\n               <jats:p>Contact: \u00a0antoniodosanjos@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformtaics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq666","type":"journal-article","created":{"date-parts":[[2010,12,3]],"date-time":"2010-12-03T01:53:52Z","timestamp":1291341232000},"page":"368-375","source":"Crossref","is-referenced-by-count":19,"title":["New approach for segmentation and quantification of two-dimensional gel electrophoresis images"],"prefix":"10.1093","volume":"27","author":[{"given":"Ant\u00f3nio","family":"dos Anjos","sequence":"first","affiliation":[{"name":"1 Department of Electronic and Informatics Engineering, University of Algarve, Faro, Portugal, 2Department of Systems Biology, Enzyme and Protein Chemistry and 3Department of Informatics and Mathematical Modelling, Technical University of Denmark, Lyngby, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anders L. B.","family":"M\u00f8ller","sequence":"additional","affiliation":[{"name":"1 Department of Electronic and Informatics Engineering, University of Algarve, Faro, Portugal, 2Department of Systems Biology, Enzyme and Protein Chemistry and 3Department of Informatics and Mathematical Modelling, Technical University of Denmark, Lyngby, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bjarne K.","family":"Ersb\u00f8ll","sequence":"additional","affiliation":[{"name":"1 Department of Electronic and Informatics Engineering, University of Algarve, Faro, Portugal, 2Department of Systems Biology, Enzyme and Protein Chemistry and 3Department of Informatics and Mathematical Modelling, Technical University of Denmark, Lyngby, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine","family":"Finnie","sequence":"additional","affiliation":[{"name":"1 Department of Electronic and Informatics Engineering, University of Algarve, Faro, Portugal, 2Department of Systems Biology, Enzyme and Protein Chemistry and 3Department of Informatics and Mathematical Modelling, Technical University of Denmark, Lyngby, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hamid R.","family":"Shahbazkia","sequence":"additional","affiliation":[{"name":"1 Department of Electronic and Informatics Engineering, University of Algarve, Faro, Portugal, 2Department of Systems Biology, Enzyme and Protein Chemistry and 3Department of Informatics and Mathematical Modelling, Technical University of Denmark, Lyngby, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,12,2]]},"reference":[{"key":"2023012511535587400_B1","doi-asserted-by":"crossref","first-page":"2735","DOI":"10.1002\/elps.1150181507","article-title":"Melanie II \u2013 a third-generation software package for analysis of two-dimensional electrophoresis images: II. algorithms","volume":"18","author":"Appel","year":"1997","journal-title":"Electrophoresis"},{"key":"2023012511535587400_B2","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1007\/s00776-004-0878-0","article-title":"Comparative evaluation of two two-dimensional gel electrophoresis image analysis software applications using synovial fluids from patients with joint disease","volume":"10","author":"Arora","year":"2005","journal-title":"J. Orthop. Sci."},{"key":"2023012511535587400_B3","article-title":"Use of watersheds in contour detection","volume-title":"International Workshop on Image Processing: Real-time Edge and Motion Detection\/Estimation.","author":"Beucher","year":"1979"},{"key":"2023012511535587400_B4","doi-asserted-by":"crossref","first-page":"3257","DOI":"10.1016\/S0006-3495(03)70050-2","article-title":"Support vector machines for predicting membrane protein types by using functional domain composition","volume":"84","author":"Cai","year":"2003","journal-title":"Biophys. J."},{"key":"2023012511535587400_B5","doi-asserted-by":"crossref","first-page":"464","DOI":"10.2174\/092986610790963654","article-title":"Predicting protein subcellular locations with feature selection and analysis","volume":"17","author":"Cai","year":"2010","journal-title":"Protein Pept. Lett."},{"key":"2023012511535587400_B6","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1186\/1471-2105-11-293","article-title":"Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition","volume":"11","author":"Chen","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012511535587400_B7","doi-asserted-by":"crossref","first-page":"45765","DOI":"10.1074\/jbc.M204161200","article-title":"Using functional domain composition and support vector machines for prediction of protein subcellular location","volume":"277","author":"Chou","year":"2002","journal-title":"J. Biol. Chem."},{"key":"2023012511535587400_B8","doi-asserted-by":"crossref","first-page":"e9931","DOI":"10.1371\/journal.pone.0009931","article-title":"A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0","volume":"5","author":"Chou","year":"2010","journal-title":"PLoS ONE"},{"key":"2023012511535587400_B9","doi-asserted-by":"crossref","first-page":"12074","DOI":"10.1016\/S0021-9258(18)80175-2","article-title":"Graphic rules in steady and non-steady state enzyme kinetics","volume":"264","author":"Chou","year":"1989","journal-title":"J. Biol. Chem."},{"key":"2023012511535587400_B10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0301-4622(90)80056-D","article-title":"Applications of graph theory to enzyme kinetics and protein folding kinetics. steady and non-steady-state systems","volume":"35","author":"Chou","year":"1990","journal-title":"Biophys. Chem."},{"key":"2023012511535587400_B11","doi-asserted-by":"crossref","first-page":"369","DOI":"10.2174\/138920010791514261","article-title":"Graphic rule for drug metabolism systems","volume":"11","author":"Chou","year":"2010","journal-title":"Curr. Drug Metab."},{"key":"2023012511535587400_B12","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1006\/abio.1994.1405","article-title":"Steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases","volume":"221","author":"Chou","year":"1994","journal-title":"Anal. Biochem."},{"key":"2023012511535587400_B13","first-page":"1","article-title":"Automatic marker detection for blob images","author":"dos Anjos","year":"2009","journal-title":"WACV'09: Proceedings of the IEEE Workshop on Applications of Computer Vision"},{"key":"2023012511535587400_B14","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1109\/TPAMI.2004.1261076","article-title":"The image foresting transform: theory, algorithms, and applications","volume":"26","author":"Falcao","year":"2004","journal-title":"IEEE Trans. Pattern Anal. Mach. Intell."},{"key":"2023012511535587400_B15","first-page":"1","article-title":"A New Marker-Based Watershed Algorithm","author":"Gao","year":"2006","journal-title":"TENCON 2006. IEEE Region 10 Conference."},{"key":"2023012511535587400_B16","doi-asserted-by":"crossref","first-page":"4958","DOI":"10.1002\/pmic.200800278","article-title":"Gel-based proteomics of gram-positive bacteria: a powerful tool to address physiological questions","volume":"8","author":"Hecker","year":"2008","journal-title":"Proteomics"},{"key":"2023012511535587400_B17","doi-asserted-by":"crossref","first-page":"e9603","DOI":"10.1371\/journal.pone.0009603","article-title":"Predicting drug-target interaction networks based on functional groups and biological features","volume":"5","author":"He","year":"2010","journal-title":"PLoS One"},{"key":"2023012511535587400_B18","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1366\/000370203322554518","article-title":"Automated method for subtraction of fluorescence from biological raman spectra","volume":"57","author":"Lieber","year":"2003","journal-title":"Appl. Spectrosc."},{"key":"2023012511535587400_B19","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1093\/bioinformatics\/btm590","article-title":"Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data","volume":"24","author":"Morris","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012511535587400_B20","doi-asserted-by":"crossref","first-page":"4007","DOI":"10.1016\/S0021-9258(19)41496-8","article-title":"High resolution 2-D electrophoresis of proteins","volume":"250","author":"O'Farrell","year":"1975","journal-title":"J. Biol. Chem."},{"key":"2023012511535587400_B21","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/0003-2697(88)90255-2","article-title":"Elsie 4: quantitative computer analysis of sets of two-dimensional gel electrophoretograms","volume":"169","author":"Olson","year":"1988","journal-title":"Anal. Biochem."},{"key":"2023012511535587400_B22","doi-asserted-by":"crossref","first-page":"5435","DOI":"10.1002\/pmic.200600273","article-title":"Proteome informatics I: Bioinformatics tools for processing experimental data","volume":"6","author":"Palagi","year":"2006","journal-title":"Proteomics"},{"key":"2023012511535587400_B23","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1186\/1471-2105-9-460","article-title":"A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics","volume":"9","author":"P\u00e8r\u00e9s","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012511535587400_B24","first-page":"187","article-title":"The watershed transform: definitions, algorithms and parallelization strategies","volume":"41","author":"Roerdink","year":"2000","journal-title":"Fundam. Inf."},{"key":"2023012511535587400_B25","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1002\/pmic.200300421","article-title":"Statistical models of shape for the analysis of protein spots in two-dimensional electrophoresis gel images","volume":"3","author":"Rogers","year":"2003","journal-title":"Proteomics"},{"key":"2023012511535587400_B26","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1002\/elps.200700418","article-title":"A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis","volume":"29","author":"Rye","year":"2008","journal-title":"Electrophoresis"},{"key":"2023012511535587400_B27","volume-title":"Morphological Image Analysis: Principles and Applications.","author":"Soille","year":"2003"},{"key":"2023012511535587400_B28","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1002\/elps.200800213","article-title":"Influence of image-analysis software on quantitation of two-dimensional gel electrophoresis data","volume":"30","author":"Stessl","year":"2009","journal-title":"Electrophoresis"},{"key":"2023012511535587400_B29","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1109\/34.87344","article-title":"Watersheds in digital spaces: An efficient algorithm based on immersion simulations","volume":"13","author":"Vincent","year":"1991","journal-title":"IEEE Trans. Pattern Anal. Mach. Intell."},{"key":"2023012511535587400_B30","doi-asserted-by":"crossref","first-page":"1090","DOI":"10.1002\/elps.11501601185","article-title":"Progress with gene-product mapping of the mollicutes: Mycoplasma genitalium","volume":"16","author":"Wasinger","year":"1995","journal-title":"Electrophoresis"},{"key":"2023012511535587400_B31","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1016\/j.jtbi.2005.02.008","article-title":"An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation","volume":"235","author":"Xiao","year":"2005","journal-title":"J. Theor. Biol."},{"key":"2023012511535587400_B32","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1016\/j.bbrc.2006.01.166","article-title":"A probability cellular automaton model for hepatitis B viral infections","volume":"342","author":"Xiao","year":"2006","journal-title":"Biochem. Biophys. Res. Commun."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/3\/368\/48862787\/bioinformatics_27_3_368.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/3\/368\/48862787\/bioinformatics_27_3_368.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T12:01:38Z","timestamp":1674648098000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/3\/368\/321053"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,12,2]]},"references-count":32,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2011,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq666","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,2,1]]},"published":{"date-parts":[[2010,12,2]]}}}