title: A novel preprocessing method using Hilbert Huang Transform for MALDI-TOF and SELDI-TOF mass spectrometry data.
abstract: BACKGROUND
  Mass spectrometry is a high throughput, fast, and accurate method of protein analysis. Using the peaks detected in spectra, we can compare a normal group with a disease group. However, the spectrum is complicated by scale shifting and is also full of noise. Such shifting makes the spectra non-stationary and need to align before comparison. Consequently, the preprocessing of the mass data plays an important role during the analysis process. Noises in mass spectrometry data come in lots of different aspects and frequencies. A powerful data preprocessing method is needed for removing large amount of noises in mass spectrometry data.
  
  
  RESULTS
  Hilbert-Huang Transformation is a non-stationary transformation used in signal processing. We provide a novel algorithm for preprocessing that can deal with MALDI and SELDI spectra. We use the Hilbert-Huang Transformation to decompose the spectrum and filter-out the very high frequencies and very low frequencies signal. We think the noise in mass spectrometry comes from many sources and some of the noises can be removed by analysis of signal frequency domain. Since the protein in the spectrum is expected to be a unique peak, its frequency domain should be in the middle part of frequency domain and will not be removed. The results show that HHT, when used for preprocessing, is generally better than other preprocessing methods. The approach not only is able to detect peaks successfully, but HHT has the advantage of denoising spectra efficiently, especially when the data is complex. The drawback of HHT is that this approach takes much longer for the processing than the wavlet and traditional methods. However, the processing time is still manageable and is worth the wait to obtain high quality data.
authors.affiliation: Graduate Institute of System Biology and Bioinformatics, National Central University, Jhongli, Taiwan. richard@mail.sybbi.ncu.edu.tw
authors.forename: Li-Ching
authors.initials: LC
authors.lastname: Wu
authors.forename: Hsin-Hao
authors.initials: HH
authors.lastname: Chen
authors.forename: Jorng-Tzong
authors.initials: JT
authors.lastname: Horng
authors.forename: Chen
authors.initials: C
authors.lastname: Lin
authors.forename: Norden E
authors.initials: NE
authors.lastname: Huang
authors.forename: Yu-Che
authors.initials: YC
authors.lastname: Cheng
authors.forename: Kuang-Fu
authors.initials: KF
authors.lastname: Cheng
mesh_terms: D003627:Data Interpretation, Statistical; D007834:Lasers; D017711:Nonlinear Dynamics; D015203:Reproducibility of Results; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D013997:Time Factors
references.citation: Bioinformatics. 2005 May 1;21(9):2088-90
references.pmid: 15691857
references.citation: Clin Chem. 2005 Jan;51(1):65-74
references.pmid: 15550476
references.citation: Nat Biotechnol. 2005 Mar;23(3):291-2
references.pmid: 15765078
references.citation: Bioinformatics. 2005 May 1;21(9):1764-75
references.pmid: 15673564
references.citation: J Proteomics. 2010 Jan 3;73(3):562-70
references.pmid: 19914411
references.citation: Biometrics. 2003 Mar;59(1):143-51
references.pmid: 12762451
references.citation: Bioinformatics. 2008 Oct 1;24(19):2129-36
references.pmid: 18694894
references.citation: Bioinformatics. 2009 Aug 1;25(15):1937-43
references.pmid: 19447788
references.citation: Biometrics. 2006 Jun;62(2):589-97
references.pmid: 16918924
references.citation: Proteomics. 2008 Aug;8(15):3019-29
references.pmid: 18615428
references.citation: Mass Spectrom Rev. 2006 May-Jun;25(3):409-49
references.pmid: 16463283
references.citation: Proc Natl Acad Sci U S A. 2007 Sep 18;104(38):14889-94
references.pmid: 17846430
references.citation: Bioinformatics. 2006 Sep 1;22(17):2059-65
references.pmid: 16820428
references.citation: Biotechniques. 2002 Mar;Suppl:34-8, 40-1
references.pmid: 11906005
references.citation: J Proteome Res. 2006 Feb;5(2):254-61
references.pmid: 16457590
references.citation: BMC Bioinformatics. 2008 Jun 11;9:275
references.pmid: 18547427
references.citation: J Biomed Inform. 2006 Apr;39(2):227-48
references.pmid: 15963765
references.citation: Mayo Clin Proc. 1989 Oct;64(10):1226-34
references.pmid: 2593713
references.citation: Expert Rev Proteomics. 2007 Jun;4(3):401-10
references.pmid: 17552924
references.citation: Proteomics. 2009 Feb;9(4):848-60
references.pmid: 19160393
references.citation: Genomics Proteomics Bioinformatics. 2007 May;5(2):77-85
references.pmid: 17893073
references.citation: BMC Bioinformatics. 2008 Feb 07;9:88
references.pmid: 18257918