The protocol is essentially your work plan and will keep the team focused throughout the systematic review process. As such, it should be developed at the onset of the systematic review process.  At the University of Pennsylvania Holman Biotech Commons, we use PRISMA which stands for the Preferred Reporting Items for Systematic Reviews and Meta-Analyses.  It is an evidence-based minimum set of items for reporting in systematic reviews and meta-analyses focusing on randomized trials.  A PRISMA flow diagram depicts the flow of information through the different phases of a systematic review.  The PRISMA 2020 checklist is an excellent resource.