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

Heidi Vähämaa, Ville R. Koskinen, Waltteri Hosia, Robert Moulder, Olli S. Nevalainen, Riitta Lahesmaa, Tero Aittokallio, Jussi Salmi, PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use. International Journal of Proteomics Vol. 2011 , 9, 2011.

http://dx.doi.org/10.1155/2011/450290

Abstract:

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.

BibTeX entry:

@ARTICLE{jVaKoHoMoNeLaAiSa11a,
  title = {PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use},
  author = {Vähämaa, Heidi and Koskinen, Ville R. and Hosia, Waltteri and Moulder, Robert and Nevalainen, Olli S. and Lahesmaa, Riitta and Aittokallio, Tero and Salmi, Jussi},
  journal = {International Journal of Proteomics},
  volume = { Vol. 2011 },
  publisher = {Hindawi Publishing Corporation },
  pages = {9},
  year = {2011},
}

Belongs to TUCS Research Unit(s): Algorithmics and Computational Intelligence Group (ACI)

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