{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T18:30:07Z","timestamp":1776277807634,"version":"3.50.1"},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Liquid chromatography coupled to mass spectrometry (LC\/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i.e. broad screening of biomolecular components across multiple samples in order to elucidate the observed phenotypes and discover biomarkers. One of the major challenges in this domain remains development of better solutions for processing of LC\/MS data.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We present a software package <jats:italic>MZmine<\/jats:italic> that enables differential LC\/MS analysis of metabolomics data. This software is a toolbox containing methods for all data processing stages preceding differential analysis: spectral filtering, peak detection, alignment and normalization. Specifically, we developed and implemented a new recursive peak search algorithm and a secondary peak picking method for improving already aligned results, as well as a normalization tool that uses multiple internal standards. Visualization tools enable comparative viewing of data across multiple samples. Peak lists can be exported into other data analysis programs. The toolbox has already been utilized in a wide range of applications. We demonstrate its utility on an example of metabolic profiling of <jats:italic>Catharanthus roseus<\/jats:italic> cell cultures.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The software is freely available under the GNU General Public License and it can be obtained from the project web page at: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/mzmine.sourceforge.net\/\">http:\/\/mzmine.sourceforge.net\/<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/1471-2105-6-179","type":"journal-article","created":{"date-parts":[[2005,7,21]],"date-time":"2005-07-21T18:13:43Z","timestamp":1121969623000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":319,"title":["Processing methods for differential analysis of LC\/MS profile data"],"prefix":"10.1186","volume":"6","author":[{"given":"Mikko","family":"Katajamaa","sequence":"first","affiliation":[]},{"given":"Matej","family":"Ore\u0161i\u010d","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2005,7,18]]},"reference":[{"key":"504_CR1","doi-asserted-by":"publisher","DOI":"10.1002\/0470867299","volume-title":"Liquid chromatography - mass spectrometry: An introduction","author":"RE Ardrey","year":"2003","unstructured":"Ardrey RE: Liquid chromatography - mass spectrometry: An introduction. , John Wiley & Sons; 2003."},{"key":"504_CR2","volume-title":"Mass spectrometry: Principles and applications","author":"E de Hoffmann","year":"2001","unstructured":"de Hoffmann E, Stroobant V: Mass spectrometry: Principles and applications. 2.th edition. , John Wiley & Sons; 2001.","edition":"2."},{"key":"504_CR3","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1038\/ng1106","volume":"33","author":"SD Patterson","year":"2003","unstructured":"Patterson SD, Aebersold RH: Proteomics: the first decade and beyond. Nat Genet 2003, 33: 311\u2013323. 10.1038\/ng1106","journal-title":"Nat Genet"},{"key":"504_CR4","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.tibtech.2004.03.007","volume":"22","author":"R Goodacre","year":"2004","unstructured":"Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB: Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 2004, 22: 245\u2013252. 10.1016\/j.tibtech.2004.03.007","journal-title":"Trends Biotechnol"},{"key":"504_CR5","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1007\/978-1-4615-0333-0_10","volume-title":"Metabolic profiling: Its role in biomarker discovery and gene function analysis","author":"J van der Greef","year":"2003","unstructured":"van der Greef J, Davidov E, Verheij E, Vogels JTWE, van der Heijden R, Adourian AS, Oresic M, Marple EW, Naylor S: The role of metabolomics in systems biology: A new vision for drug discovery and development. In Metabolic profiling: Its role in biomarker discovery and gene function analysis. Edited by: Harrigan GG and Goodacre R. Boston, Mass., Kluwer Academic Publishers; 2003:171\u2013198."},{"key":"504_CR6","doi-asserted-by":"publisher","first-page":"205","DOI":"10.2165\/00822942-200403040-00002","volume":"3","author":"M Oresic","year":"2004","unstructured":"Oresic M, Clish CB, Davidov EJ, Verheij E, Vogels JTWE, Havekes LM, Neumann E, Adourian A, Naylor S, Greef J, Plasterer T: Phenotype characterization using integrated gene transcript, protein and metabolite profiling. Appl Bioinformatics 2004, 3: 205\u2013217.","journal-title":"Appl Bioinformatics"},{"key":"504_CR7","unstructured":"Organization HP: mzData.[http:\/\/psidev.sourceforge.net\/ms\/#mzdata]"},{"key":"504_CR8","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1089\/omi.2004.8.267","volume":"8","author":"E Davidov","year":"2004","unstructured":"Davidov E, Clish CB, Oresic M, Meys M, Stochaj W, Snell P, Lavine G, Londo TR, Adourian A, Zhang X, Johnston M, Morel N, Marple EW, Plasterer TN, Neumann E, Verheij E, Vogels JTWE, Havekes LM, Greef J, Naylor S: Methods for the differential integrative omic analysis of plasma from a transgenic disease animal model. OMICS A Journal of Integrative Biology 2004, 8: 267\u2013288. 10.1089\/omi.2004.8.267","journal-title":"OMICS A Journal of Integrative Biology"},{"key":"504_CR9","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1002\/(SICI)1099-128X(199609)10:5\/6<425::AID-CEM442>3.0.CO;2-S","volume":"10","author":"JTWE Vogels","year":"1996","unstructured":"Vogels JTWE, Tas AC, Venekamp J, Greef J: Partial linear fit : a new NMR spectroscopy preprocessing tool for pattern recognition applications. J Chemometrics 1996, 10: 425\u2013438. Publisher Full Text 10.1002\/(SICI)1099-128X(199609)10:5\/6%3C425::AID-CEM442%3E3.0.CO;2-S","journal-title":"J Chemometrics"},{"key":"504_CR10","doi-asserted-by":"publisher","first-page":"4818","DOI":"10.1021\/ac026468x","volume":"75","author":"W Wang","year":"2003","unstructured":"Wang W, Zhou H, Lin H, Roy S, Shaler TA, Hill LR, Norton S, Kumar P, Anderle M, Becker CH: Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 2003, 75: 4818 -44826. 10.1021\/ac026468x","journal-title":"Anal Chem"},{"key":"504_CR11","doi-asserted-by":"publisher","first-page":"984","DOI":"10.1074\/mcp.M400061-MCP200","volume":"3","author":"D Radulovic","year":"2004","unstructured":"Radulovic D, Jelveh S, Ryu S, Hamilton TG, Foss E, Mao Y, Emili A: Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 2004, 3: 984\u2013997. 10.1074\/mcp.M400061-MCP200","journal-title":"Mol Cell Proteomics"},{"key":"504_CR12","unstructured":"Lewis JP, Neumann U: Performance of Java versus C++.[http:\/\/www.idiom.com\/~zilla\/Computer\/javaCbenchmark.html]"},{"key":"504_CR13","unstructured":"UniData NetCDF[http:\/\/my.unidata.ucar.edu\/content\/software\/netcdf\/index.html]"},{"key":"504_CR14","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1038\/nbt1031","volume":"22","author":"PGA Pedrioli","year":"2004","unstructured":"Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R: A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 2004, 22: 1459\u20131466. 10.1038\/nbt1031","journal-title":"Nat Biotechnol"},{"key":"504_CR15","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1023\/A:1013713905833","volume":"48","author":"O Fiehn","year":"2002","unstructured":"Fiehn O: Metabolomics - the link between genotyopes and phenotypes. Plant Molecular Biology 2002, 48: 155\u2013171. 10.1023\/A:1013713905833","journal-title":"Plant Molecular Biology"},{"key":"504_CR16","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1016\/j.tplants.2004.07.006","volume":"9","author":"KM Oksman-Caldentey","year":"2004","unstructured":"Oksman-Caldentey KM, Inze D: Plant cell factories in the post-genomic era: new ways to produce designer secondary metabolites. Trends Plant Sci 2004, 9: 433\u2013440. 10.1016\/j.tplants.2004.07.006","journal-title":"Trends Plant Sci"},{"key":"504_CR17","series-title":"Biotechnology in Agriculture and Forrestry","volume-title":"Plant metabolomics","author":"M Oresic","year":"2005","unstructured":"Oresic M, Rischer H, Oksman-Caldentey KM: Metabolomics of plant secondary compounds: profiling of Catharanthus cell cultures. Biotechnology in Agriculture and Forrestry. In Plant metabolomics. Edited by: Saito K, Willmitzer L and Dixon D. Heidelberg, Springer Verlag, in press; 2005."},{"key":"504_CR18","doi-asserted-by":"publisher","DOI":"10.1002\/0471725331","volume-title":"User's guide to principal components","author":"JE Jackson","year":"1991","unstructured":"Jackson JE: User's guide to principal components. New York, NY, John Wiley & Sons; 1991."},{"key":"504_CR19","doi-asserted-by":"publisher","first-page":"1595","DOI":"10.1023\/B:BILE.0000045825.37395.94","volume":"26","author":"CW Lee-Parsons","year":"2004","unstructured":"Lee-Parsons CW, Ert\u00fcrk S, Tengtrakool J: Enhancement of ajmalicine production in Catharanthus roseus cell cultures with methyl jasmonate is dependent on timing and dosage of elicitation. Biotechnol Lett 2004, 26: 1595\u20131599. 10.1023\/B:BILE.0000045825.37395.94","journal-title":"Biotechnol Lett"},{"key":"504_CR20","doi-asserted-by":"publisher","first-page":"1706","DOI":"10.2337\/diabetes.54.6.1706","volume":"54","author":"G Medina-Gomez","year":"2005","unstructured":"Medina-Gomez G, Virtue S, Lelliott C, Boiani R, Campbell M, Christodoulides C, Perrin C, Jimenez-Linan M, Blount M, Dixon J, Zahn D, Thresher RR, Aparicio S, Carlton M, Colledge WH, Kettunen MI, Seppanen-Laakso T, Sethi JK, O'Rahilly S, Brindle K, Cinti S, Oresic M, Burcelin R, Vidal-Puig A: The link between nutritional status and insulin sensitivity is dependent on the adipocyte-specific Peroxisome Proliferator-Activated Receptor-{gamma}2 isoform. Diabetes 2005, 54: 1706\u20131716.","journal-title":"Diabetes"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-179.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T17:56:08Z","timestamp":1706810168000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-179"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,7,18]]},"references-count":20,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["504"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-179","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,7,18]]},"assertion":[{"value":"8 March 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 July 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 July 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"179"}}