Abstract
Motivation: The combination of liquid chromatography and mass spectrometry (LC/MS) has been widely used for large-scale comparative studies in systems biology, including proteomics, glycomics and metabolomics. In almost all experimental design, it is necessary to compare chromatograms across biological or technical replicates and across sample groups. Central to this is the peak alignment step, which is one of the most important but challenging preprocessing steps. Existing alignment tools do not take into account the structural dependencies between related peaks that coelute and are derived from the same metabolite or peptide. We propose a direct matching peak alignment method for LC/MS data that incorporates related peaks information (within each LC/MS run) and investigate its effect on alignment performance (across runs). The groupings of related peaks necessary for our method can be obtained from any peak clustering method and are built into a pair-wise peak similarity score function. The similarity score matrix produced is used by an approximation algorithm for the weighted matching problem to produce the actual alignment result.Results: We demonstrate that related peak information can improve alignment performance. The performance is evaluated on a set of benchmark datasets, where our method performs competitively compared to other popular alignment tools.Availability: The proposed alignment method has been implemented as a stand-alone application in Python, available for download at http://github.com/joewandy/peak-grouping-alignment.Contact: Simon.Rogers@glasgow.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
Liquid chromatography, coupled to mass spectrometry (LC/MS) is one of the most widely used techniques in untargeted proteomic and metabolomic studies (Vandenbogaert et al, 2008)
We addressed the lack of comparative evaluation of alignment tools as discussed in Smith et al (2013) by independently reproducing key results from Lange et al (2008) and Voss et al (2011) for the Join and Simultaneous Multiple Alignment (SIMA) alignment methods
We have proposed a novel peak matching method that incorporates related peak information to improve alignment performance
Summary
Liquid chromatography, coupled to mass spectrometry (LC/MS) is one of the most widely used techniques in untargeted proteomic and metabolomic studies (Vandenbogaert et al, 2008). Compounds in the mixture are separated in time through liquid chromatography (LC) and subjected to mass spectrometry (MS) analysis. The result of this process is a mass chromatogram: an intensity surface across the mass-to-charge ratio (m/z) and retention time (RT) dimensions. From this surface, it is possible to extract individual peaks (corresponding to ions in the mass spectrometry).
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