A new method for alignment of LC-MALDI-TOF data

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. © 2011 tang et al; licensee biomed central ltd.