Recent developments have shown the emergence of electronic negotiation systems and electronic markets used to efficiently allocate electronic resources, such as web services. Electronic negotiations exhibit much of the same problems real life negotiations have, such as coalition formation, efficient offer matching etc. However, some problems become more crucial in electronic environments due to the anonymity of the users and the sheer amount of negotiations that can be executed in short time spans. In this paper we investigate the trust issue in electronic negotiations, dealing with how to trust a potential transaction partner and how to choose such partners based on their past behaviour in the system. In particular, we want to investigate the efficiency or even applicability of reputation mechanisms for different negotiation protocols and market flavors. Based on social science findings we derive hypotheses on the effects of various commonly used negotiation protocols on the efficient usage of reputation mechanism. We conclude with a set of such hypotheses that can be used to give recommendations to designers of electronic negotiation systems or markets on which protocols to use, so that they can apply reputation mechanisms and therefore tackle the trusting issue.