Similar protocols

Protocol publication

[…] ion (alignment) for multivariate analysis ., There are generally two types of alignment algorithms, i.e. a local merge strategy and a global merge strategy. The former commonly employs three techniques, warping , , , , , , nearest neighbour , and clustering , , . These are generally computationally efficient, but typically scan spectra one by one to generate consensuses, which cannot be updated or revised. Consequently the first scans may generate a false consensus based on an incorrect feature set which cannot subsequently be revised when “correct” features are scanned later , . Many alignment tools, both commercial ones and freeware, belong to this type e.g. MetAlign , MSFACTs , OPenMS . Binbase , MathDAMP , ChromA , LC-MSsim , XCMS , SpecAlign , MET-IDEA ., In order to increase alignment accuracy we recently developed PAD (Peak Alignment via Density maximisation), which adopted a global merge strategy using a concept called the Map Coverage Maximization (MCM), where a `map’ refers to a spectrum. It implements a novel alignment principle, i.e. density maximisation. Among various overlapping candidate consensuses, a consensus with the highest density is selected as the prediction. A consensus refers to the prediction of a true, but unknown metabolite. However PAD is comparatively much slower than a local merge algorithm such as implemented by SIMA , which is typical to a global merge algorithm., […]

Pipeline specifications

Software tools BinBase, MathDAMP, ChromA