title: Improved candidate biomarker detection based on mass spectrometry data using the Hilbert-Huang transform.
abstract: Mass spectrometry biomarker discovery may assist patient's diagnosis in time and realize the characteristics of new diseases. Our previous work built a preprocess method called HHTmass which is capable of removing noise, but HHTmass only a proof of principle to be peak detectable and did not tested for peak reappearance rate and used on medical data. We developed a modified version of biomarker discovery method called Enhance HHTMass (E-HHTMass) for MALDI-TOF and SELDI-TOF mass spectrometry data which improved old HHTMass method by removing the interpolation and the biomarker discovery process. E-HHTMass integrates the preprocessing and classification functions to identify significant peaks. The results show that most known biomarker can be found and high peak appearance rate achieved comparing to MSCAP and old HHTMass2. E-HHTMass is able to adapt to spectra with a small increasing interval. In addition, new peaks are detected which can be potential biomarker after further validation.
authors.affiliation: Graduate Institute of System Biology and Bioinformatics, National Central University, JhongLi City, Taoyuan County, Taiwan. richard@mail.sybbi.ncu.edu.tw
authors.forename: Li-Ching
authors.initials: LC
authors.lastname: Wu
authors.forename: Ping-Heng
authors.initials: PH
authors.lastname: Hsieh
authors.forename: Jorng-Tzong
authors.initials: JT
authors.lastname: Horng
authors.forename: Yu-Jen
authors.initials: YJ
authors.lastname: Jou
authors.forename: Chia-Der
authors.initials: CD
authors.lastname: Lin
authors.forename: Kuang-Fu
authors.initials: KF
authors.lastname: Cheng
authors.forename: Cheng-Wen
authors.initials: CW
authors.lastname: Lin
authors.forename: Shih-Yin
authors.initials: SY
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D023181:Antimicrobial Cationic Peptides / Q000652:urine; D001327:Autoimmune Diseases / Q000097:blood / Q000175:diagnosis; D015415:Biomarkers / Q000378:metabolism*; D019295:Computational Biology; D057225:Data Mining; D016208:Databases, Factual; D064451:Hepcidins; D006801:Humans; D007674:Kidney Diseases / Q000175:diagnosis / Q000378:metabolism; D009062:Mouth Neoplasms / Q000175:diagnosis / Q000378:metabolism; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D023181:Antimicrobial Cationic Peptides; D015415:Biomarkers; D064451:Hepcidins