title: A new method for alignment of LC-MALDI-TOF data.
abstract: 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).
  
  
  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.
authors.affiliation: Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA. hwr@georgetown.edu.
authors.forename: Zhiqun
authors.initials: Z
authors.lastname: Tang
authors.forename: Lihua
authors.initials: L
authors.lastname: Zhang
authors.forename: Amrita K
authors.initials: AK
authors.lastname: Cheema
authors.forename: Habtom W
authors.initials: HW
authors.lastname: Ressom