Delay Tolerant Networking (DTN) architecture is a new communication architecture developed to provide network connectivity in challenging environments. It forms a store-and-forward overlay network that employs persistent storage to deal with link disconnections. Consistent with its store-and-forward requirements, the design of the transport function of the DTN architecture was primarily based on hop-by-hop operations in preference to the traditional end-to-end communication model. As a result, pure end-to-end functionality is absent from the current DTN architecture and thus has been shifted towards applications. In this study, we highlight the benefits of having an additional layer of application-independent protocol offering transparent application data conditioning services end-to-end and we introduce Delay Tolerant Payload Conditioning (DTPC) protocol, a novel protocol that realizes this layer. DTPC protocol is an expandable, connectionless, reliable, sequenced transport protocol which extends the DTN architecture in a fashion that accords with the end-to-end principle, enabling the following services: (a) application data aggregation, (b) application-level reliability, (c) in-order delivery, and (d) duplicate suppression. DTPC was integrated into the JPL's Interplanetary Overlay Network (ION) DTN reference implementation, and its functionality was evaluated/validated through real-time experiments in a DTN testbed.