The Draft report on the provision of usage data and manuscript deposit procedures for publishers and repository managers, deliverable 2.1, set out to establish a workflow for depositing stage-2 outputs in and harvesting log files from repositories to enable the research envisaged in the PEER project. As that report preceded the tendering process whereby the respective research teams were selected, a number of issues were flagged for attention, particularly of the Usage research team, in WP5 and have since been referred for consultation. A significant outcome of the previous draft report was the recommendation to establish the PEER Depot as a closed intermediary repository, to receive publisher deposit in the form of both 50% of the full-text outputs, as well as 100% of the metadata outputs; and to serve as a base line control for the research process. The PEER Depot has since been established, and has come to play a significant role in the workflow developed. While the draft report set out a preliminary deposit workflow from publishers to repositories, the central role of the PEER Depot has since influenced further developments in the provision of usage data and manuscript deposit procedures for both publishers and authors. This report is the result of an ongoing negotiation between stakeholder groups comprising publishers and the library/repository community to establish best practice in deposit proce- dures that are least disruptive of existing publication workflows, while minimizing additional effort in repository ingest activities