{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T16:34:12Z","timestamp":1759336452628},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"S4","license":[{"start":{"date-parts":[[2016,2,1]],"date-time":"2016-02-01T00:00:00Z","timestamp":1454284800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2016,2]]},"DOI":"10.1186\/s12859-016-0911-2","type":"journal-article","created":{"date-parts":[[2016,3,2]],"date-time":"2016-03-02T06:31:38Z","timestamp":1456900298000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Geena 2, improved automated analysis of MALDI\/TOF mass spectra"],"prefix":"10.1186","volume":"17","author":[{"given":"Paolo","family":"Romano","sequence":"first","affiliation":[]},{"given":"Aldo","family":"Profumo","sequence":"additional","affiliation":[]},{"given":"Mattia","family":"Rocco","sequence":"additional","affiliation":[]},{"given":"Rosa","family":"Mangerini","sequence":"additional","affiliation":[]},{"given":"Fabio","family":"Ferri","sequence":"additional","affiliation":[]},{"given":"Angelo","family":"Facchiano","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,3,2]]},"reference":[{"issue":"7","key":"911_CR1","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1016\/j.jprot.2010.03.001","volume":"73","author":"M D\u2019Imperio","year":"2010","unstructured":"D\u2019Imperio M, Della Corte A, Facchiano A, Di Michele M, Ferrandina G, Donati MB, et al. Standardized sample preparation phases for a quantitative measurement of plasma peptidome profiling by MALDI-TOF. J Proteomics. 2010;73(7):1355\u201367. doi: 10.1016\/j.jprot.2010.03.001 . PMID: 20227539.","journal-title":"J Proteomics"},{"issue":"3","key":"911_CR2","doi-asserted-by":"publisher","first-page":"e0120932","DOI":"10.1371\/journal.pone.0120932","volume":"10","author":"M Mitchell","year":"2015","unstructured":"Mitchell M, Mali S, King CC, Bark SJ. Enhancing MALDI time-of-flight mass spectrometer performance through spectrum averaging. PLoS One. 2015;10(3):e0120932. doi: 10.1371\/journal.pone.0120932 . PMID: 25798583.","journal-title":"PLoS One"},{"issue":"2","key":"911_CR3","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.ab.2011.06.021","volume":"417","author":"R Mangerini","year":"2011","unstructured":"Mangerini R, Romano P, Facchiano A, Damonte G, Muselli M, Rocco M, et al. The application of atmospheric pressure MALDI to the analysis of long-term cryopreserved serum peptidome. Anal Biochem. 2011;417(2):174\u201381. doi: 10.1016\/j.ab.2011.06.021 . PMID: 21756868.","journal-title":"Anal Biochem"},{"key":"911_CR4","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.jprot.2013.04.029","volume":"85","author":"A Profumo","year":"2013","unstructured":"Profumo A, Mangerini R, Rubagotti A, Romano P, Damonte G, Guglielmini P, et al. Complement C3f serum levels may predict breast cancer risk in women with gross cystic disease of the breast. J Proteomics. 2013;85:44\u201352. doi: 10.1016\/j.jprot.2013.04.029 . PMID: 23639844.","journal-title":"J Proteomics"},{"issue":"12","key":"911_CR5","doi-asserted-by":"publisher","first-page":"872","DOI":"10.3109\/09513590.2014.943718","volume":"30","author":"RA Siciliano","year":"2014","unstructured":"Siciliano RA, Mazzeo MF, Spada V, Facchiano A, D\u2019Acierno A, Stocchero M, et al. Rapid peptidomic profiling of peritoneal fluid by MALDI-TOF mass spectrometry for the identification of biomarkers of endometriosis. Gynecol Endocrinol. 2014;30(12):872\u20136. doi: 10.3109\/09513590.2014.943718 . PMID: 25111755.","journal-title":"Gynecol Endocrinol"},{"key":"911_CR6","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1016\/j.mib.2014.06.014","volume":"19","author":"J Fang","year":"2014","unstructured":"Fang J, Dorrestein PC. Emerging mass spectrometry techniques for the direct analysis of microbial colonies. Curr Opin Microbiol. 2014;19:120\u20139. doi: 10.1016\/j.mib.2014.06.014 . PMID: 25064218.","journal-title":"Curr Opin Microbiol"},{"issue":"2","key":"911_CR7","doi-asserted-by":"publisher","first-page":"1180","DOI":"10.1128\/AEM.72.2.1180-1189.2006","volume":"72","author":"MF Mazzeo","year":"2006","unstructured":"Mazzeo MF, Sorrentino A, Gaita M, Cacace G, Di Stasio M, Facchiano A, et al. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the discrimination of food-borne microorganisms. Appl Environ Microbiol. 2006;72(2):1180\u20139. doi: 10.1128\/AEM.72.2.1180-1189.2006 . PMID: 16461665.","journal-title":"Appl Environ Microbiol"},{"issue":"23","key":"911_CR8","doi-asserted-by":"publisher","first-page":"11071","DOI":"10.1021\/jf8021783","volume":"56","author":"MF Mazzeo","year":"2008","unstructured":"Mazzeo MF, De Giulio B, Guerriero G, Ciarcia G, Malorni A, Russo GL, et al. Fish authentication by MALDI-TOF mass spectrometry. J Agric Food Chem. 2008;56(23):11071\u20136. doi: 10.1021\/jf8021783 . PMID: 19007297.","journal-title":"J Agric Food Chem"},{"issue":"2","key":"911_CR9","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1002\/jms.3538","volume":"50","author":"C Dhieb","year":"2015","unstructured":"Dhieb C, Normand AC, L\u2019Olliver C, Gautier M, Vranckx K, El Euch D, et al. Comparison of MALDI-TOF mass spectra with microsatellite length polymorphisms in Candida albicans. J Mass Spectrom. 2015;50(2):371\u20137. doi: 10.1002\/jms.3538 . PMID: 25800019.","journal-title":"J Mass Spectrom"},{"key":"911_CR10","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/1756-6606-6-60","volume":"6","author":"JP Salisbury","year":"2013","unstructured":"Salisbury JP, Boggio KJ, Hsu YW, Quijada J, Sivachenko A, Gloeckner G, et al. A rapid MALDI-TOF mass spectrometry workflow for Drosophila melanogaster differential neuropeptidomics. Mol Brain. 2013;6:60. doi: 10.1186\/1756-6606-6-60 . PMID: 24373546.","journal-title":"Mol Brain"},{"issue":"A","key":"911_CR11","doi-asserted-by":"crossref","first-page":"125","DOI":"10.14806\/ej.18.A.454","volume":"18","author":"P Romano","year":"2012","unstructured":"Romano P, Profumo A, Mangerini R, Ferri F, Rocco M, Boccardo F, et al. Geena, a tool for MS spectra filtering, averaging and aligning. EMBnet J. 2012;18(A):125\u20136. 10.14806\/ej.18.A.454.","journal-title":"EMBnet J"},{"key":"911_CR12","unstructured":"PHP: Hypertext Preprocessor. http:\/\/php.net\/ . Accessed 1 February 2016."},{"key":"911_CR13","unstructured":"The Perl Programming Language. http:\/\/www.perl.org\/ . Accessed 1 February 2016."},{"key":"911_CR14","unstructured":"NEAPOLIS. http:\/\/bioinformatica.isa.cnr.it\/NEAPOLIS\/ . Accessed 1 February 2016."},{"key":"911_CR15","unstructured":"MySQL :: The world\u2019s most popular open source database. http:\/\/www.mysql.com\/ . Accessed 1 February 2016."},{"key":"911_CR16","unstructured":"Molecular Weight Calculator for Windows. http:\/\/www.alchemistmatt.com\/mwtwin.html . Accessed 1 February 2016."},{"issue":"10","key":"911_CR17","doi-asserted-by":"publisher","first-page":"2394","DOI":"10.1002\/ijc.29609","volume":"137","author":"F Boccardo","year":"2015","unstructured":"Boccardo F, Rubagotti A, Nuzzo PV, Argellati F, Savarino G, Romano P, et al. Matrix-assisted laser desorption\/ionisation (MALDI) TOF analysis identifies serum Angiotensin II concentrations as a strong predictor of all-cause and breast cancer (Bca)-specific mortality following breast surgery. Int J Cancer. 2015;137(10):2394\u2013402. doi: 10.1002\/ijc.29609 . PMID: 25994113.","journal-title":"Int J Cancer"},{"key":"911_CR18","unstructured":"LabVIEW System Design Software - National Instruments. http:\/\/www.ni.com\/labview\/ . Accessed 1 February 2016."},{"key":"911_CR19","unstructured":"Geena 2: MS-BASELINER. http:\/\/bioinformatics.hsanmartino.it\/geena2\/background.php . Accessed 1 February 2016."},{"issue":"Suppl 1","key":"911_CR20","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/1477-5956-9-S1-S10","volume":"9","author":"Z Tang","year":"2011","unstructured":"Tang Z, Zhang L, Cheema AK, Ressom HW. A new method for alignment of LC-MALDI-TOF data. Proteome Sci. 2011;9 Suppl 1:10. doi: 10.1186\/1477-5956-9-S1-S10 . PMID: 22166061.","journal-title":"Proteome Sci"},{"issue":"9","key":"911_CR21","doi-asserted-by":"publisher","first-page":"2088","DOI":"10.1093\/bioinformatics\/bti300","volume":"21","author":"JW Wong","year":"2005","unstructured":"Wong JW, Cagney G, Cartwright HM. SpecAlign \u2013 processing and alignement of mass spectra. Bioinformatics. 2005;21(9):2088\u201390. doi: 10.1093\/bioinformatics\/bti300 . PMID: 15691857.","journal-title":"Bioinformatics"},{"key":"911_CR22","unstructured":"mzML 1.1.0 Specification | HUPO Proteomics Standards Initiative. http:\/\/www.psidev.info\/mzml_1_0_0 . Accessed 1 February 2016."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-0911-2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T03:22:39Z","timestamp":1498274559000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-0911-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,2]]},"references-count":22,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2016,2]]}},"alternative-id":["911"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-0911-2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,2]]},"article-number":"61"}}