Similar protocols

Pipeline publication

[…] teps is out of the scope of the present paper. The interested reader should refer to the documentation of each specific software package or to some comprehensive software review [e.g., Katajamaa and Oresic (), Castillo et al. ()]. As a general consideration, however, it is important to say that all the algorithms have advantages and limitations. For this reason, there is no ultimate solution, and – as always in metabolomics – it is necessary to find a good compromise. Vendor-specific softwares are provided by all the instrument manufacturers, and it is also possible to rely on cross-platform solutions like the open-source MZmine (Pluskal et al., ) and OpenMS (Sturm et al., ) or the freeware MetAlign (Lommen, )., Some of these approaches have a graphical user interface; others can be implemented in graphical software suites or web-based interfaces to make them easily accessible to the lab scientist. As already discussed, however, graphical interactive tools are not ideal for pipelines, and scriptable solutions are to be preferred. Among these, a place of merit is held by the R [R Core Team ()] package XCMS (Smith et al., ). The development of the software started in 2006 and has gained momentum in the last years, also thanks to several ancillary R packages, which have been expanding its functionalities. The fact that it is written in R makes its integration with cutting-edge statistical packages trivial. Recently, the XCMS development team has been working on the integration of XCMS with ISA-Tab (González-Beltrán et al., )., Also, feature grouping can be performed by different algorithms, e.g., the correlation-based R package CAMERA (Kuhl et al., ) and the clustering-based MSclust software (Tikunov et al., )., The association of (groups of) experimental features to specific metabolites is commonly referred as “annotation” and it is, most likely, the biggest challenge for untargeted metabolomics experiments (Brown et al., ; Neumann and Böcker, ; Prasad et al., ; Dunn et al., ). As in the case of the meta information, the Metabolomic Standard Initiative recommends minimum reporting standards for annotation. The guidelines propose four different “confidence” levels of annotation. They go from “Identified Compounds” – for which the identification is confirmed by a comparison with the results of the analysis of a pure chemical standard – to “Unknown” – in the cases […]

Pipeline specifications

Software tools MetAlign, XCMS, MSClust