%0 Journal Article
%T A new method for alignment of LC-MALDI-TOF data
%A Tang Zhiqun
%A Zhang Lihua
%A Cheema Amrita K
%A Ressom Habtom W
%J Proteome Science
%D 2011
%I BioMed Central
%R 10.1186/1477-5956-9-s1-s10
%X Background In proteomics studies, liquid chromatography coupled to mass spectrometry (LC-MS) has proven to be a powerful technology to investigate differential expression of proteins/peptides that are characterized by their peak intensities, mass-to-charge ratio (m/z), and retention time (RT). The variable complexity of peptide mixtures and occasional drifts lead to substantial variations in m/z and RT dimensions. Thus, label-free differential protein expression studies by LC-MS technology require alignment with respect to both RT and m/z to ensure that same proteins/peptides are compared from multiple runs. Methods In this study, we propose a new strategy to align LC-MALDI-TOF data by combining quality threshold cluster analysis and support vector regression. Our method performs alignment on the basis of measurements in three dimensions (RT, m/z, intensity). Results and conclusions We demonstrate the suitability of our proposed method for alignment of LC-MALDI-TOF data through a previously published spike-in dataset and a new in-house generated spike-in dataset. A comparison of our method with other methods that utilize only RT and m/z dimensions reveals that the use of intensity measurements enhances alignment performance.
%U http://www.math.hkbu.edu.hk/BIBM2010/index.html