A general-purpose baseline estimation algorithm for spectroscopic data

Analytica Chimica Acta

Volumn 657, Issue 2, 2010, Pages 191-197

  Barkauskas, Donald A ^a   Rocke, David M ^b  

^a CHILDREN S ONCOLOGY GROUP   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Baseline estimation; Fourier transform ion cyclotron resonance; Matrix assisted laser desorption ionization; Spectroscopy

Indexed keywords

ANALYTIC TOOLS; BACKGROUND NOISE; BASELINE ESTIMATION; COMMON FEATURES; COMPUTATIONALLY EFFICIENT; FOURIER TRANSFORM ION CYCLOTRON RESONANCE; FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETRY; FT-ICR MS; LARGE AMOUNTS OF DATA; MATRIX ASSISTED LASER DESORPTION/IONIZATION; MODERN APPLICATIONS; MODERN TECHNOLOGIES; PROTEOMICS; SIGNAL EXTRACTION; SPECTROSCOPIC DATA;

ALGORITHMS; CYCLOTRONS; DESORPTION; ELECTRON CYCLOTRON RESONANCE; ESTIMATION; IONS; LASERS; MAGNETIC RESONANCE IMAGING; MASS SPECTROMETERS; MASS SPECTROMETRY; MATRIX ALGEBRA; MOLECULAR BIOLOGY; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PLASMAS; PROTEINS; RADIOACTIVITY MEASUREMENT; RESONANCE; SIGNAL PROCESSING;

FOURIER TRANSFORMS;

ALGORITHM; ANALYTIC METHOD; ARTICLE; DATA ANALYSIS; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; MASS SPECTROMETRY; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL PARAMETERS; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEOMICS; REFERENCE VALUE;

ALGORITHMS; MAGNETIC RESONANCE SPECTROSCOPY; PROTEOMICS; SIGNAL PROCESSING, COMPUTER-ASSISTED; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 71249113613     PISSN: 00032670     EISSN: 18734324     Source Type: Journal    
DOI: 10.1016/j.aca.2009.10.043     Document Type: Article

References (16)

1. Xi Y., and Rocke D. Baseline correction for NMR spectroscopic metabolomics data analysis. BMC Bioinf. 9 1 (2008) 324
2. Coombes K.R., Tsavachidis S., Morris J., Baggerly K., Hung M.-C., and Kuerer H. 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 5 16 (2005) 4107-4117
3. Du P., Sudha R., Prystowsky M.B., and Angeletti R.H. Data reduction of isotope-resolved LC-MS spectra. Bioinformatics 23 11 (2007) 1394-1400
4. Mantini D., Petrucci F., Pieragostino D., Del Boccio P., Di Nicola M., Di Ilio C., Federici G., Sacchetta P., Comani S., and Urbani A. LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise. BMC Bioinf. 8 1 (2007) 101
5. Karpievitch Y.V., Hill E.G., Smolka A.J., Morris J.S., Coombes K.R., Baggerly K.A., and Almeida J.S. PrepMS: TOF MS data graphical preprocessing tool. Bioinformatics 23 2 (2007) 264-265
6. Li X., Gentleman R., Lu X., Shi Q., Iglehart J.D., Harris L., and Miron A. Proteomics spectra. In: Gentleman R., Carey V., Huber W., Irizarry R., and Dudoit S. (Eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor (2005), Springer 91-109
7. Bellew M., Coram M., Fitzgibbon M., Igra M., Randolph T., Wang P., May D., Eng J., Fang R., Lin C., Chen J., Goodlett D., Whiteaker J., Paulovich A., and McIntosh M. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 22 15 (2006) 1902-1909
8. Yasui Y., Pepe M., Thompson M.L., Adam B.-L., Wright J., George L., Qu Y., Potter J.D., Winget M., Thornquist M., and Feng Z. A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection. Biostatastics 4 3 (2003) 449-463
9. Du P., Kibbe W.A., and Lin S.M. Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics 22 17 (2006) 2059-2065
10. Lange E., Gröpl C., Reinert K., Kohlbacher O., and Hildebrandt A. High-accuracy peak picking of proteomics data using wavelet techniques. Pac. Symp. Biocomput. 11 (2006) 243-254
11. Zhang L.-K., Rempel D., Pramanik B.N., and Gross M.L. Accurate mass measurements by Fourier transform mass spectrometry. Mass Spectrom. Rev. 24 2 (2005) 286-309
12. Barkauskas D.A., Kronewitter S.R., Lebrilla C.B., and Rocke D.M. Analysis of MALDI FT-ICR mass spectrometry data: A time series approach. Anal. Chim. Acta 648 2 (2009) 207-214
13. Herbert C.G., and Johnstone R.A.W. Mass Spectrometry Basics (2003), CRC Press, Boca Raton, FL
14. Park Y., and Lebrilla C.B. Application of Fourier transform ion cyclotron resonance mass spectrometry to oligosaccharides. Mass Spectrom. Rev. 24 2 (2005) 232-264
15. Barkauskas D.A., An H.J., Kronewitter S.R., de Leoz M.L., Chew H.K., de Vere White R.W., Leiserowitz G.S., Miyamoto S., Lebrilla C.B., and Rocke D.M. Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data. Bioinformatics 25 2 (2009) 251-257
16. Yang C., He Z., and Yu W. Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis. BMC Bioinf. 10 1 (2009) 4