Project members

• Péter Horvatovich (owner)
• Berend Hoekman

Welcome to project LCMS_time_alignment_algorithms

Background

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.

References:

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

Mailing lists

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).

Source access

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.

You can become a developer by  registering yourself if you haven't already done so, and requesting write access on the  lcms_time_alignment_algorithms-users mailing list.

Starting Points

• TracGuide -- Built-in Documentation
• TitleIndex -- A complete list of local wiki pages.
•  Trac FAQ -- Frequently Asked Questions

Other NBIC software projects

All active NBIC software projects can be accessed from the  project index.