Last modified 5 years ago Last modified on 08-03-11 21:32:26

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Welcome to project LCMS_time_alignment_algorithms



This project contains Matlab code of various LC-MS time alignment functions taking account mass dimension in the procedure to correct for non-linear retention time shifts between chromatograms. The time alignment approaches are combining Correlation Optimized Warping (COW), Dynamic Time Warping (DTW) and Parametric Time Warping (PTW) with COmponent Detection Algorithm (CODA) and are described in details in the references (1) and (2). All functions take as input two raw LC-MS data files resampled in regular mesh, and provide the corrected retention time vector of the mesh of the sample chromatogram aligned to the reference chromatogram. Example LC-MS datafile are provided in the download section and example parameters and alignment procedure is presented in runwarp.m script. This project was reaslised within NBIC Biorange SP 2.2.3 entitled "Biostatistics for proteomics and metabolomics based clinical biomarker discovery." and is take part of the Gaining Momentum Initiative, which is a join effort of NBIC and NPC to advance proteomics related bioinformatics.


1 Christin C, Hoefsloot HC, Smilde AK, Suits F, Bischoff R, Horvatovich PL., Time alignment algorithms based on selected mass traces for complex LC-MS data, J Proteome Res., 2010, 9(3):1483-1495. PMID: 20070124
2 Christin C, Smilde AK, Hoefsloot HC, Suits F, Bischoff R, Horvatovich PL., Optimized time alignment algorithm for LC-MS data: correlation optimized warping using component detection algorithm-selected mass chromatograms, Anal Chem., 2008, 80(18):7012-7021. PMID: 18715018

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Anonymous readonly subversion access works as follows:

  svn co lcms_time_alignment_algorithms

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