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
This project provides the following mailing lists.
- lcms_time_alignment_algorithms-users: a list intended for general discussion on the project.
- lcms_time_alignment_algorithms-commits: a list that receives source code commit messages.
- lcms_time_alignment_algorithms-devel: a list intended for discussion among developers (subscription is restricted to registered developers).
Anonymous readonly subversion access works as follows:
svn co https://trac.nbic.nl/svn/lcms_time_alignment_algorithms lcms_time_alignment_algorithms
Write access is only available to registered developers.
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- Trac FAQ -- Frequently Asked Questions
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