Abstract
Mass spectrometry (MS) is becoming the gold standard for biomarker discovery. Several MS-based bioinformatics methods have been proposed for this application, but the divergence of the findings by different research groups on the same MS data suggests that the definition of a reliable method has not been achieved yet. In this work, we propose an integrated software platform, MASCAP, intended for comparative biomarker detection from MALDI-TOF MS data. MASCAP integrates denoising and feature extraction algorithms, which have already shown to provide consistent peaks across mass spectra; furthermore, it relies on statistical analysis and graphical tools to compare the results between groups. The effectiveness in mass spectrum processing is demonstrated using MALDI-TOF data, as well as SELDI-TOF data. The usefulness in detecting potential protein biomarkers is shown comparing MALDI-TOF mass spectra collected from serum and plasma samples belonging to the same clinical population. The analysis approach implemented in MASCAP may simplify biomarker detection, by assisting the recognition of proteomic expression signatures of the disease. A MATLAB implementation of the software and the data used for its validation are available at http...Continue Reading
References
Aug 20, 2003·Biostatistics·Yutaka YasuiZiding Feng
Nov 15, 2003·Journal of Biomedicine & Biotechnology·Yutaka YasuiZiding Feng
Jan 8, 2004·Clinical Chemistry and Laboratory Medicine : CCLM·Pierre-Alain BinzRon D Appel
Mar 3, 2004·Molecular & Cellular Proteomics : MCP·Eleftherios P Diamandis
May 28, 2004·Rapid Communications in Mass Spectrometry : RCM·Martin KempkaJohan Roeraade
Jun 26, 2004·Bioinformatics·Glen A SattenJohn R Barr
Nov 6, 2004·Nature Biotechnology·Patrick G A PedrioliRuedi Aebersold
May 10, 2005·Bioinformatics·Neal Jeffries
May 26, 2005·Clinica Chimica Acta; International Journal of Clinical Chemistry·Gianluca MaddaloGiorgio Federici
Jun 30, 2005·Proteomics·Jens LamerzHans-Dieter Zucht
Aug 9, 2005·Journal of Proteome Research·Josep VillanuevaPaul Tempst
Oct 29, 2005·Proteomics·Kevin R CoombesHenry M Kuerer
Apr 29, 2006·Clinical Chemistry·Glen L Hortin
Jul 6, 2006·Bioinformatics·Pan DuSimon M Lin
Nov 4, 2006·Proteomics·Shen HuDavid T Wong
Mar 28, 2007·BMC Bioinformatics·Dante MantiniAndrea Urbani
Mar 29, 2007·Proteomics·Scott M CarlsonHarvey J Cohen
Jul 10, 2007·Molecular & Cellular Proteomics : MCP·Amol PrakashBenno Schwikowski
Sep 21, 2007·Proteomics·Margriet M W B HendriksAge K Smilde
Nov 16, 2007·Bioinformatics·Dante MantiniAndrea Urbani
Aug 12, 2009·Journal of Proteomics·Damiana PieragostinoAndrea Urbani
Feb 8, 2013·Journal of Clinical Microbiology·Tai-Fen LeePo-Ren Hsueh
Jan 1, 2005·Drug Discovery Today. Technologies·Nils von Neuhoff, Andreas Pich
Citations
Aug 19, 2011·Parasitology Research·Lixia LiQuan Liu
Mar 28, 2012·Vector Borne and Zoonotic Diseases·Jiping LiJun Qian
Sep 21, 2011·Clinical Proteomics·Dong L TongGraham R Ball
Sep 9, 2010·PloS One·Li-Ching WuKuang-Fu Cheng
Dec 4, 2012·International Journal of Molecular Sciences·Siyan ZhaoLinna Liu
Feb 20, 2014·Food Microbiology·Carola C KernJürgen Behr
Apr 5, 2014·Journal of Pharmaceutical and Biomedical Analysis·Miguel Angel Merlos RodrigoRene Kizek
Mar 13, 2014·Applied Microbiology and Biotechnology·Julia C UsbeckRudi F Vogel
Feb 12, 2013·Chemical Reviews·Jeremy L Norris, Richard M Caprioli
Jul 15, 2015·Clinica Chimica Acta; International Journal of Clinical Chemistry·Joanna HajdukZenon J Kokot
Jan 16, 2013·Proteomics·Damiana PieragostinoAndrea Urbani
Nov 16, 2013·Critical Reviews in Microbiology·Chunlei ShiAndrea Isabel Moreno Switt
Dec 6, 2014·Food Microbiology·Benjamin C SchurrRudi F Vogel
Dec 6, 2014·Food Microbiology·Benjamin C SchurrRudi F Vogel
Oct 27, 2016·PloS One·Ann-Sophie SchottRudi F Vogel
Jan 20, 2018·Proteomics. Clinical Applications·Sachio TsuchidaFumio Nomura
Mar 10, 2018·Rapid Communications in Mass Spectrometry : RCM·Pavel CejnarBarbora Svobodova
Mar 4, 2018·Scientific Reports·Ana C O NevesKássio M G Lima
Mar 14, 2019·Journal of Applied Microbiology·M HilgarthR F Vogel
Aug 10, 2017·PloS One·Alexander LauterbachRudi F Vogel
Jan 12, 2011·Journal of Food Protection·Ji-Yeon HyeonKun-Ho Seo
Nov 8, 2011·Journal of Food Protection·L L KudraK J Prusa
Oct 26, 2016·Molecular Medicine Reports·Shaoyu YangShenglin Ma
Dec 15, 2017·Journal of Applied Microbiology·M HilgarthR F Vogel
Aug 8, 2021·Microorganisms·Eva Torres-SangiaoCarlos García-Riestra
Jan 18, 2022·Applied Microbiology and Biotechnology·Monika K ForsterLudwig Niessen