Response to desk return of PLOS submission I recently submitted to PLOS One.  The manuscript was returned before sending to review, with a general comment


  Please ensure that your search strategy is adequately described such
  that another researcher could reproduce your experiments. Please
  include sufficient detail to this end. Eg, search strategy/protocol,
  search filters used, the dates of search, inclusion/exclusion
  criteria, reasons for inclusion/exclusion


The paper uses Web of Science.  The search terms and methods are simple and detailed in full.  I am confused if there was something specific they are wondering about, or more important, if they assume there was some additional criteria or method used.  For example, downloading all data with search term "Graphene" using the Topic search box.  I am not sure what else they would think is being done.

PLOS being particularly open access, I understand the extra focus on the methods, but is this a common response?  Is it usual they did not read the manuscript and just skimmed it, and I should reply with line numbers of where it exists?  

I don't believe it is really an issue of the manuscript not stating it clearly, as it is its own subsection in methods detailed in each step.
Check if you have covered all the details that the editor has mentioned. If you are very sure that there is no scope for adding any other detail, you can write to the editor, providing a point by point explanation of what you have done, with page numbers and line numbers as evidence. Since the manuscript has anyways been rejected, you do not stand to lose anything by doing this. However, ensure that you maintain a polite and courteous tone throughout your email. Your email should not give the impression that you are refuting the editor's decision; rather, it should seem like you are seeking more clarity on the weaknesses of your paper, so that you can work towards improving it.