apLCMS-adaptive processing of high-resolution LC/MS data

被引:288
作者
Yu, Tianwei [1 ]
Park, Youngja [2 ]
Johnson, Jennifer M. [2 ]
Jones, Dean P. [2 ]
机构
[1] Emory Univ, Rollins Sch Publ Hlth, Dept Biostat & Bioinformat, Atlanta, GA 30322 USA
[2] Emory Univ, Sch Med, Dept Med, Atlanta, GA USA
关键词
MASS-SPECTROMETRY; PEAK DETECTION; ALIGNMENT; MS; METABOLOMICS; METABONOMICS; METABOLITES; ALGORITHMS;
D O I
10.1093/bioinformatics/btp291
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Liquid chromatography-mass spectrometry (LC/MS) pro. ling is a promising approach for the quanti. cation of metabolites from complex biological samples. Significant challenges exist in the analysis of LC/MS data, including noise reduction, feature identification/quantification, feature alignment and computation efficiency. Result: Here we present a set of algorithms for the processing of high-resolution LC/MS data. The major technical improvements include the adaptive tolerance level searching rather than hard cutoff or binning, the use of non-parametric methods to. ne-tune intensity grouping, the use of run filter to better preserve weak signals and the model-based estimation of peak intensities for absolute quanti. cation. The algorithms are implemented in an R package apLCMS, which can efficiently process large LC/MS datasets.
引用
收藏
页码:1930 / 1936
页数:7
相关论文
共 24 条
[1]   Feature detection and alignment of hyphenated chromatographic-mass spectrometric data -: Extraction of pure ion chromatograms using Kalman tracking [J].
Aberg, K. Magnus ;
Torgrip, Ralf J. O. ;
Kolmert, Johan ;
Schuppe-Koistinen, Ina ;
Lindberg, Johan .
JOURNAL OF CHROMATOGRAPHY A, 2008, 1192 (01) :139-146
[2]   MathDAMP: a package for differential analysis of metabolite profiles [J].
Baran, Richard ;
Kochi, Hayataro ;
Saito, Natsumi ;
Suematsu, Makoto ;
Soga, Tomoyoshi ;
Nishioka, Takaaki ;
Robert, Martin ;
Tomita, Masaru .
BMC BIOINFORMATICS, 2006, 7 (1)
[3]   A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS [J].
Bellew, Matthew ;
Coram, Marc ;
Fitzgibbon, Matthew ;
Igra, Mark ;
Randolph, Tim ;
Wang, Pei ;
May, Damon ;
Eng, Jimmy ;
Fang, Ruihua ;
Lin, ChenWei ;
Chen, Jinzhi ;
Goodlett, David ;
Whiteaker, Jeffrey ;
Paulovich, Amanda ;
McIntosh, Martin .
BIOINFORMATICS, 2006, 22 (15) :1902-1909
[4]   Metabolite identification via the Madison Metabolomics Consortium Database [J].
Cui, Qiu ;
Lewis, Ian A. ;
Hegeman, Adrian D. ;
Anderson, Mark E. ;
Li, Jing ;
Schulte, Christopher F. ;
Westler, William M. ;
Eghbalnia, Hamid R. ;
Sussman, Michael R. ;
Markley, John L. .
NATURE BIOTECHNOLOGY, 2008, 26 (02) :162-164
[5]   Mass spectrometry-based metabolomics [J].
Dettmer, Katja ;
Aronov, Pavel A. ;
Hammock, Bruce D. .
MASS SPECTROMETRY REVIEWS, 2007, 26 (01) :51-78
[6]   Data reduction of isotope-resolved LC-MS spectra [J].
Du, Peicheng ;
Sudha, Rajagopalan ;
Prystowsky, Michael B. ;
Angeletti, Ruth Hogue .
BIOINFORMATICS, 2007, 23 (11) :1394-1400
[7]   New algorithms for processing and peak detection in liquid chromatography/mass spectrometry data [J].
Hastings, CA ;
Norton, SM ;
Roy, S .
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 2002, 16 (05) :462-467
[8]   Screening of biomarkers in rat urine using LC/electrospray ionization-MS and two-way data analysis [J].
Idborg-Björkman, H ;
Edlund, PO ;
Kvalheim, OM ;
Schuppe-Koistinen, I ;
Jacobsson, SP .
ANALYTICAL CHEMISTRY, 2003, 75 (18) :4784-4792
[9]   MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data [J].
Katajamaa, M ;
Miettinen, J ;
Oresic, M .
BIOINFORMATICS, 2006, 22 (05) :634-636
[10]   Data processing for mass spectrometry-based metabolomics [J].
Katajamaa, Mikko ;
Oresic, Matej .
JOURNAL OF CHROMATOGRAPHY A, 2007, 1158 (1-2) :318-328