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Although label-free approaches allow for flexible experimental designs, they are often associated with rigorous analytical and informatic requirements, including: attention to reproducibility of sample preparation and chromatographic separations; automation of multiple LC-MS file alignment; and automation of precursor ion detection and quantitation.
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However, end users are still in need of authoritatively vetted alignments to make real-world queries and discoveries, and automation is not without its drawbacks and limitations (7).
Most likely this is done in order to obtain speed or because automation of multiple alignment and phylogeny was deemed unfeasible.
In contrast, although they have been shown to exhibit greater accuracy and lower error rates than pairwise comparison methods, phylogeny based approaches have been only partially exploited due to the complexity of the automation of sequence alignment and the choice of appropriate genes and species to be included in the analysis [ 42, 43].
Although the dataset presented in this study is limited to small number of genes, the methodology presented of using shared single copy genes for phylogenetics using sequences from public databases could be expanded to utilize all of the shared single copy nuclear genes with automation of the alignment and sequence selection methods.
Death and automation.
Robotics and Automation, 2001.
Robotics and Automation, 2004.
IEEE International Conference on Robotics and Automation (ICRA).
Conf. on Robotics and Automation - ICRA, 2015.
Robotics and Automation, 2008.
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