MPA: A multiple peak alignment algorithm to perform multiple comparisons of liquid‐phase proteomic profiles

Abstract

Present proteomic studies increasingly address experimental strategies focused on multiple comparisons of proteomic profiles. To accomplish semiautomatic protein separations based on 2-D LC, the Beckman Coulter PF2D has been developed. Here, we present a novel general purpose tool called MPA (multiple peak alignment) able to perform multiple comparisons of proteomic profiles both in a pairwise guided fashion and in a fully automatic mode using a strategy based on dynamic programing and progressive alignment of time series. The tool is available at http://grup.cribi.unipd.it/people/stefano/mpa/.

Differential liquid phase proteomic analysis of the effect of selenium supplementation in LNCaP cells

“…control and different supplementation conditions). In the latter case, for repetition of experiments, we used a multiple alignment program specifically developed to this aim [19].…”

Mass Spectrometry Analysis Using MALDIquant

“…An alternative, and much more flexible approach, is Dynamic Time Warping (DTW) which is based on dynamic programming (Torgrip et al, 2003;Toppoo et al, 2008;Clifford et al, 2009;Kim et al, 2011). DTW is a pairwise alignment approach that is guaranteed to find the optimal alignment by comparing each point in the first spectrum to every other point in the second spectrum, and optimizing a distance score.…”

Warping and alignment technologies for inter-sample feature correspondence in 1D H-NMR, chromatography-, and capillary electrophoresis-mass spectrometry data

“…Shifting peaks will be blurred or even lost if averaging over NMR spectra or TICs, XICs (or other 1D representation) is used for a synthetic target creation. Some papers use hybrid methods to avoid specifying a reference: successive sample pair-wise alignments [74,75].…”