Discretionary Revisions The authors have presented a DIMS and LC-MS metabolomics data processing and analysis workflow. It is clear that a substantial amount of work has gone into not just building this workflow, but also in developing the different components over the years that have been used in this solution. In presenting this solution as a Galaxy workflow, the authors have shown their intent to potentially integrate with the other omics’ solutions and workflow that are already present in Galaxy. This is an important step towards the development of a systems wide solution. One of the biggest strengths of the proposed solution as I see is the exhaustive number of options presented to the user to set parameters along every step of the processing workflow. However, for users to best benefit from this, I would recommend that the authors develop a user guide with detailed instructions and explanations of every step using an example data (and data of intermediate steps) such that the user clearly see how the input data is transformed all the way through the workflow. Such a user guide would make the proposed solution very usable. Also, as the authors’ have indicated as future work, I believe the proposed solution would improve vastly through the addition of further statistical analysis tools – a univariate analysis module as a minimum. Strengthening the statistical analysis part of the workflow would make the solution complete and hence make it more attractive for the community to adopt this solution.

Overall, the authors have presented an excellent solution for the processing of DIMS and LC-MS metabolomics data and I believe this solution would benefit the Metabolomics community greatly.

Level of interest:

An article of importance in its field

Quality of written English:

Acceptable

Statistical review:

Yes, and I have assessed the statistics in my report.

Declaration of competing interests: I declare that I have no competing interests.

Authors' response to reviews: (http://www.gigasciencejournal.com/imedia/7048735118495094_comment.pdf)

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/1623648222162780_manuscript.pdf
All revised versions are also available:
Draft - http://www.gigasciencejournal.com/imedia/1623648222162780_manuscript.pdf