Table of Contents
International Journal of Proteomics
Volume 2011, Article ID 450290, 9 pages
Research Article

PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use

1Department of Information Technology, University of Turku, 20014 Turun yliopisto, Finland
2Turku Centre for Computer Science, Joukahaisenkatu 3-5 B, 6th floor, FI-20520 Turku, Finland
3Karolinska Institutet, SE-171 77 Stockholm, Sweden
4Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland
5Department of Mathematics, University of Turku, Finland

Received 4 November 2010; Revised 10 January 2011; Accepted 9 February 2011

Academic Editor: Michael Hippler

Copyright © 2011 Heidi Vähämaa et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


We present a versatile user-friendly software tool, PolyAlign, for the alignment of multiple LC-MS signal maps with the option of manual landmark setting or automated alignment. One of the spectral images is selected as a reference map, and after manually setting the landmarks, the program warps the images using either polynomial or Hermite transformation. The software provides an option for automated landmark finding. The software includes a very fast zoom-in function synchronized between the images, which facilitate detecting correspondences between the adjacent images. Such an interactive visual process enables the analyst to decide when the alignment is satisfactory and to correct known irregularities. We demonstrate that the software provides significant improvements in the alignment of LC-MALDI data, with 10–15 landmark pairs, and it is also applicable to correcting electrospray LC-MS data. The results with practical data show substantial improvement in peak alignment compared to MZmine, which was among the best analysis packages in a recent assessment. The PolyAlign software is freely available and easily accessible as an integrated component of the popular MZmine software, and also as a simpler stand-alone Perl implementation to preview data and apply landmark directed polynomial transformation.