LC–MS-based holistic metabolic profiling. Problems, limitations, advantages, and future perspectives

• A review of the advantages, constrains and issues in MS-based metabolomics.
• Perspective for future research seen in six fields.
• Design of experiment, analytical developments for quality control-validation, improvement of metabolome coverage, fusion of data, metabolite identification, and data visualisation.

The present review aims to critically discuss some of the major problems and limitations of LC–MS based metabolomics as experienced from an analytical chemistry standpoint. Metabolomics offers distinct advantages to a variety of life sciences. Continuous development of the field has been realised due to intensive efforts from a great many scientists from widely divergent backgrounds and research interests as demonstrated by the contents of this special issue. The aim of this commentary is to describe current hindrances to field's progress, (some unique to metabolomics, some common with other omics fields or with conventional targeted bioanalysis) to propose some potential solutions to overcome these constraints and to provide a future perspective for likely developments in the field.