{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T21:29:54Z","timestamp":1761514194817,"version":"3.41.0"},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,4,5]],"date-time":"2018-04-05T00:00:00Z","timestamp":1522886400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"BHI-PRO project, ANR","award":["ANR 2010 BLAN 0313"],"award-info":[{"award-number":["ANR 2010 BLAN 0313"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2116-3","type":"journal-article","created":{"date-parts":[[2018,4,19]],"date-time":"2018-04-19T14:29:50Z","timestamp":1524148190000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Linear MALDI-ToF simultaneous spectrum deconvolution and baseline removal"],"prefix":"10.1186","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0108-8433","authenticated-orcid":false,"given":"Vincent","family":"Picaud","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Francois","family":"Giovannelli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caroline","family":"Truntzer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Philippe","family":"Charrier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Audrey","family":"Giremus","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Grangeat","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Catherine","family":"Mercier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,4,5]]},"reference":[{"issue":"6","key":"2116_CR1","doi-asserted-by":"publisher","first-page":"475","DOI":"10.3343\/alm.2017.37.6.475","volume":"37","author":"A van Belkum","year":"2017","unstructured":"van Belkum A, Welker M, Pincus D, Charrier JP, Girard V. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiology: What are the current issues?Ann Lab Med. 2017; 37(6):475.","journal-title":"Ann Lab Med"},{"issue":"1","key":"2116_CR2","doi-asserted-by":"publisher","first-page":"75","DOI":"10.2353\/jmoldx.2009.080079","volume":"11","author":"EN Ilina","year":"2009","unstructured":"Ilina EN, Borovskaya AD, Malakhova MM, Vereshchagin VA, Kubanova AA, Kruglov AN, Svistunova TS, Gazarian AO, Maier T, Kostrzewa M, Govorun VM. Direct bacterial profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for identification of pathogenic neisseria. J Mol Diagn. 2009; 11(1):75\u201386.","journal-title":"J Mol Diagn"},{"key":"2116_CR3","doi-asserted-by":"publisher","unstructured":"Singhal N, Kumar M, Kanaujia PK, Virdi JS. Maldi-tof mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol. 2015; 6:791. https:\/\/doi.org\/10.3389\/fmicb.2015.00791 .","DOI":"10.3389\/fmicb.2015.00791"},{"issue":"1","key":"2116_CR4","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1471-2105-10-4","volume":"10","author":"C Yang","year":"2009","unstructured":"Yang C, He Z, Yu W. Comparison of public peak detection algorithms for maldi mass spectrometry data analysis. BMC Bioinformatics. 2009; 10(1):4.","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"2116_CR5","doi-asserted-by":"publisher","first-page":"4201","DOI":"10.1021\/ac401048d","volume":"85","author":"CK Larive","year":"2013","unstructured":"Larive CK, Sweedler JV. Celebrating the 75th anniversary of the acs division of analytical chemistry: A special collection of the most highly cited analytical chemistry papers published between 1938 and 2012. Anal Chem. 2013; 85(9):4201\u20132.","journal-title":"Anal Chem"},{"issue":"8","key":"2116_CR6","doi-asserted-by":"publisher","first-page":"1627","DOI":"10.1021\/ac60214a047","volume":"36","author":"A Savitzky","year":"1964","unstructured":"Savitzky A, Golay MJ. Smoothing and differentiation of data by simplified least squares procedures. Anal Chem. 1964; 36(8):1627\u201339.","journal-title":"Anal Chem"},{"issue":"6","key":"2116_CR7","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1021\/ac00205a007","volume":"62","author":"PA Gorry","year":"1990","unstructured":"Gorry PA. General least-squares smoothing and differentiation by the convolution (savitzky-golay) method. Anal Chem. 1990; 62(6):570\u20133.","journal-title":"Anal Chem"},{"issue":"1","key":"2116_CR8","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.dsp.2006.01.006","volume":"17","author":"M Browne","year":"2007","unstructured":"Browne M, Mayer N, Cutmore TR. A multiscale polynomial filter for adaptive smoothing. Digit Signal Process. 2007; 17(1):69\u201375.","journal-title":"Digit Signal Process"},{"issue":"17","key":"2116_CR9","doi-asserted-by":"publisher","first-page":"2758","DOI":"10.1021\/ac00113a006","volume":"67","author":"P Barak","year":"1995","unstructured":"Barak P. Smoothing and differentiation by an adaptive-degree polynomial filter. Anal Chem. 1995; 67(17):2758\u201362.","journal-title":"Anal Chem"},{"issue":"10","key":"2116_CR10","doi-asserted-by":"publisher","first-page":"2464","DOI":"10.1109\/78.157290","volume":"40","author":"MJ Shensa","year":"1992","unstructured":"Shensa MJ. The discrete wavelet transform: wedding the a trous and mallat algorithms. IEEE Trans Signal Process. 1992; 40(10):2464\u201382.","journal-title":"IEEE Trans Signal Process"},{"key":"2116_CR11","doi-asserted-by":"publisher","unstructured":"Nason GP, Silverman BW. The stationary wavelet transform and some statistical applications In: Antoniadis A, Oppenheim G, editors. Wavelets and Statistics. New York: Springer: 1995. p. 281\u201399. https:\/\/doi.org\/10.1007\/978-1-4612-2544-7_17 .","DOI":"10.1007\/978-1-4612-2544-7_17"},{"key":"2116_CR12","doi-asserted-by":"publisher","first-page":"4107","DOI":"10.1002\/pmic.200401261","volume":"5","author":"KR Coombes","year":"2005","unstructured":"Coombes KR, Tsavachidis S, Morris JS, Baggerly KA, Kuerer HM. Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. Proteomics. 2005; 5:4107\u201317.","journal-title":"Proteomics"},{"issue":"1","key":"2116_CR13","first-page":"17","volume":"151","author":"A Antoniadis","year":"2010","unstructured":"Antoniadis A, Bigot J, Lambert-Lacroix S. Peaks detection and alignment for mass spectrometry data. J Soci\u00e9t\u00e9 Fran\u00e7aise Stat. 2010; 151(1):17\u201337.","journal-title":"J Soci\u00e9t\u00e9 Fran\u00e7aise Stat"},{"issue":"6","key":"2116_CR14","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1366\/000370210791414281","volume":"64","author":"R Perez-Pueyo","year":"2010","unstructured":"Perez-Pueyo R, Soneira MJ, Ruiz-Moreno S. Morphology-based automated baseline removal for raman spectra of artistic pigments. Appl Spectrosc. 2010; 64(6):595\u2013600.","journal-title":"Appl Spectrosc"},{"issue":"1","key":"2116_CR15","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1366\/000370208783412762","volume":"62","author":"M Morh\u00e1\u010d","year":"2008","unstructured":"Morh\u00e1\u010d M, Matou\u0161ek V. Peak clipping algorithms for background estimation in spectroscopic data. Appl Spectrosc. 2008; 62(1):91\u2013106.","journal-title":"Appl Spectrosc"},{"issue":"2","key":"2116_CR16","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.chemolab.2004.10.003","volume":"76","author":"V Mazet","year":"2005","unstructured":"Mazet V, Carteret C, Brie D, Idier J, Humbert B. Background removal from spectra by designing and minimising a non-quadratic cost function. Chemometr Intell Lab Syst. 2005; 76(2):121\u201333.","journal-title":"Chemometr Intell Lab Syst"},{"issue":"2","key":"2116_CR17","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1016\/S0022-4073(00)00021-2","volume":"68","author":"AF Ruckstuhl","year":"2001","unstructured":"Ruckstuhl AF, Jacobson MP, Field RW, Dodd JA. Baseline subtraction using robust local regression estimation. J Quant Spectrosc Radiative Transf. 2001; 68(2):179\u201393.","journal-title":"J Quant Spectrosc Radiative Transf"},{"issue":"16","key":"2116_CR18","doi-asserted-by":"publisher","first-page":"4483","DOI":"10.1039\/c3an00743j","volume":"138","author":"Z Li","year":"2013","unstructured":"Li Z, Zhan DJ, Wang JJ, Huang J, Xu QS, Zhang ZM, Zheng YB, Liang YZ, Wang H. Morphological weighted penalized least squares for background correction. Analyst. 2013; 138(16):4483\u201392.","journal-title":"Analyst"},{"key":"2116_CR19","first-page":"9","volume":"3","author":"J Dubrovkin","year":"2014","unstructured":"Dubrovkin J. Evaluation of the peak location uncertainty in second-order derivative spectra. Case study: symmetrical lines. J Emerg Technol Comput Appl Sci. 2014; 3:9.","journal-title":"J Emerg Technol Comput Appl Sci"},{"issue":"1","key":"2116_CR20","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/S1387-3806(01)00562-0","volume":"215","author":"A Mohammad-Djafari","year":"2002","unstructured":"Mohammad-Djafari A, Giovannelli JF, Demoment G, Idier J. Regularization, maximum entropy and probabilistic methods in mass spectrometry data processing problems. Int J Mass Spectrom. 2002; 215(1):175\u201393.","journal-title":"Int J Mass Spectrom"},{"issue":"1","key":"2116_CR21","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1186\/1471-2105-9-355","volume":"9","author":"BY Renard","year":"2008","unstructured":"Renard BY, Kirchner M, Steen H, Steen JA, Hamprecht FA. Nitpick: peak identification for mass spectrometry data. BMC Bioinformatics. 2008; 9(1):355.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"2116_CR22","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1186\/1471-2105-13-291","volume":"13","author":"M Slawski","year":"2012","unstructured":"Slawski M, Hussong R, Tholey A, Jakoby T, Gregorius B, Hildebrandt A, Hein M. Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares\/least absolute deviation template matching. BMC Bioinformatics. 2012; 13(1):291.","journal-title":"BMC Bioinformatics"},{"key":"2116_CR23","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1051\/0004-6361:20047011","volume":"439","author":"JF Giovannelli","year":"2005","unstructured":"Giovannelli JF, Coulais A. Positive deconvolution for superimposed extended source and point sources. Astron Astrophys. 2005; 439:401\u201312.","journal-title":"Astron Astrophys"},{"issue":"3","key":"2116_CR24","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1089\/cmb.2010.0264","volume":"18","author":"M Hirsch","year":"2011","unstructured":"Hirsch M, Sch\u00f6lkopf B, Habeck M. A blind deconvolution approach for improving the resolution of cryo-em density maps. J Comput Biol. 2011; 18(3):335\u201346.","journal-title":"J Comput Biol"},{"key":"2116_CR25","doi-asserted-by":"crossref","unstructured":"Lange E, Gr\u00f6pl C, Reinert K, Kohlbacher O, Hildebrandt A. High-Accuracy Peak Picking Of Proteomics Data Using Wavelet Techniques. In: Biocomputing 2006. World Scientific: 2012. p. 243\u201354. https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/9789812701626_0023 .","DOI":"10.1142\/9789812701626_0023"},{"issue":"17","key":"2116_CR26","doi-asserted-by":"publisher","first-page":"2059","DOI":"10.1093\/bioinformatics\/btl355","volume":"22","author":"P Du","year":"2006","unstructured":"Du P, Kibbe WA, Lin SM. Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics. 2006; 22(17):2059\u201365.","journal-title":"Bioinformatics"},{"key":"2116_CR27","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1109\/34.142909","volume":"7","author":"S Mallat","year":"1992","unstructured":"Mallat S, Zhong S. Characterization of signals from multiscale edges. IEEE Trans Pattern Anal Mach Intell. 1992; 7:710\u201332.","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"issue":"4","key":"2116_CR28","doi-asserted-by":"publisher","first-page":"586","DOI":"10.1109\/JSTSP.2007.910281","volume":"1","author":"MA Figueiredo","year":"2007","unstructured":"Figueiredo MA, Nowak RD, Wright SJ. Gradient projection for sparse reconstruction: Application to compressed sensing and other inverse problems. IEEE J Sel Top Sign Process. 2007; 1(4):586\u201397.","journal-title":"IEEE J Sel Top Sign Process"},{"key":"2116_CR29","doi-asserted-by":"crossref","unstructured":"Tibshirani R. Regression shrinkage and selection via the lasso. J R Stat Soc Ser B Methodol. 1996; 58(1):267\u201388. http:\/\/www.jstor.org\/stable\/2346178 .","DOI":"10.1111\/j.2517-6161.1996.tb02080.x"},{"issue":"1","key":"2116_CR30","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1007\/s00211-004-0569-y","volume":"100","author":"YH Dai","year":"2005","unstructured":"Dai YH, Fletcher R. Projected barzilai-borwein methods for large-scale box-constrained quadratic programming. Numer Math. 2005; 100(1):21\u201347.","journal-title":"Numer Math"},{"issue":"1","key":"2116_CR31","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1093\/imanum\/8.1.141","volume":"8","author":"J Barzilai","year":"1988","unstructured":"Barzilai J, Borwein JM. Two-point step size gradient methods. IMA J Numer Anal. 1988; 8(1):141\u20138.","journal-title":"IMA J Numer Anal"},{"key":"2116_CR32","volume-title":"Optimization and Control with Applications","author":"R Fletcher","year":"2005","unstructured":"Fletcher R. On the barzilai-borwein method In: Qi L, Teo K, Yang X, editors. Optimization and Control with Applications. Boston: Springer US: 2005. p. 235\u201356."},{"issue":"1","key":"2116_CR33","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1137\/S1052623494266365","volume":"7","author":"M Raydan","year":"1997","unstructured":"Raydan M. The barzilai and borwein gradient method for the large scale unconstrained minimization problem. SIAM J Optim. 1997; 7(1):26\u201333.","journal-title":"SIAM J Optim"},{"issue":"3","key":"2116_CR34","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1093\/imanum\/13.3.321","volume":"13","author":"M Raydan","year":"1993","unstructured":"Raydan M. On the barzilai and borwein choice of steplength for the gradient method. IMA J Numer Anal. 1993; 13(3):321\u20136.","journal-title":"IMA J Numer Anal"},{"issue":"1","key":"2116_CR35","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1137\/0801008","volume":"1","author":"JJ Mor\u00e9","year":"1991","unstructured":"Mor\u00e9 JJ, Toraldo G. On the solution of large quadratic programming problems with bound constraints. SIAM J Optim. 1991; 1(1):93\u2013113.","journal-title":"SIAM J Optim"},{"key":"2116_CR36","doi-asserted-by":"crossref","unstructured":"Kim D, Sra S, Dhillon IS. A non-monotonic method for large-scale non-negative least squares. Optim Methods Softw (OMS). 2012.","DOI":"10.1080\/10556788.2012.656368"},{"issue":"4","key":"2116_CR37","doi-asserted-by":"publisher","first-page":"1196","DOI":"10.1137\/S1052623497330963","volume":"10","author":"EG Birgin","year":"2000","unstructured":"Birgin EG, Mart\u00ednez JM, Raydan M. Nonmonotone spectral projected gradient methods on convex sets. SIAM J Optim. 2000; 10(4):1196\u2013211.","journal-title":"SIAM J Optim"},{"key":"2116_CR38","unstructured":"Boyd S, Vandenberghe L. Convex optimization.Cambridge university press; 2009."},{"key":"2116_CR39","doi-asserted-by":"publisher","unstructured":"Mercier C, Klich A, Truntzer C, Picaud V, Giovannelli J-F, Ducoroy P, Grangeat P, Maucort-Boulch D, Roy P. Variance component analysis to assess protein quantification in biomarker discovery. application to MALDI-TOF mass spectrometry. Biom J. 2017; 60(2):262\u201374. https:\/\/doi.org\/10.1002\/bimj.201600198 .","DOI":"10.1002\/bimj.201600198"},{"issue":"3","key":"2116_CR40","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1016\/0168-583X(88)90063-8","volume":"34","author":"C Ryan","year":"1988","unstructured":"Ryan C, Clayton E, Griffin W, Sie S, Cousens D. Snip, a statistics-sensitive background treatment for the quantitative analysis of pixe spectra in geoscience applications. Nucl Inst Methods Phys Res Sec B: Beam Interactions with Mater Atoms. 1988; 34(3):396\u2013402.","journal-title":"Nucl Inst Methods Phys Res Sec B: Beam Interactions with Mater Atoms"},{"issue":"1","key":"2116_CR41","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/S0168-9002(97)01023-1","volume":"401","author":"M Morh\u00e1\u010d","year":"1997","unstructured":"Morh\u00e1\u010d M, Kliman J, Matou\u0161ek V, Veselsky\u0300 M, Turzo I. Background elimination methods for multidimensional coincidence \u03b3-ray spectra. Nucl Inst Methods Phys Res Sec A: Accelerators, Spectrometers, Detectors and Assoc Equip. 1997; 401(1):113\u201332.","journal-title":"Nucl Inst Methods Phys Res Sec A: Accelerators, Spectrometers, Detectors and Assoc Equip"},{"issue":"17","key":"2116_CR42","doi-asserted-by":"publisher","first-page":"2270","DOI":"10.1093\/bioinformatics\/bts447","volume":"28","author":"S Gibb","year":"2012","unstructured":"Gibb S, Strimmer K. Maldiquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics. 2012; 28(17):2270\u20131.","journal-title":"Bioinformatics"},{"key":"2116_CR43","unstructured":"Conte SD, Boor CWD. Elementary numerical analysis: an algorithmic approach: McGraw-Hill High Educ.1980."},{"key":"2116_CR44","doi-asserted-by":"publisher","unstructured":"Varga RS. Ger\u0161gorin and his circles: Springer Berlin Heidelberg; 2004. https:\/\/doi.org\/10.1007\/978-3-642-17798-9 .","DOI":"10.1007\/978-3-642-17798-9"},{"key":"2116_CR45","first-page":"134","volume":"7","author":"BN Parlett","year":"1980","unstructured":"Parlett BN. The symmetric eigenvalue problem. SIAM. 1980; 7:134.","journal-title":"SIAM"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2116-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2116-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2116-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,3]],"date-time":"2025-07-03T19:46:45Z","timestamp":1751572005000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2116-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,4,5]]},"references-count":45,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2116"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2116-3","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2018,4,5]]},"assertion":[{"value":"13 July 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 March 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 April 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"JPC is employed by bioM\u00e9rieux. The other authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"123"}}