This methodological paper describes how qualitative data analysis software (QDAS) is being used to manage and support a three-step protocol analysis (PA) of think aloud (TA) data in a study examining emergency nurses' reasoning during triage. The authors believe that QDAS program QRS NVivo will greatly facilitate the PA and will allow them to identify and describe the information that triage nurses concentrate on during triage, and how they structure this information to make a triage decision. These findings could assist in designing and creating decision support systems to guide nurses' triaging. Additionally, details about how to use QRS NVivo for PA of TA data may assist and guide future informatics research using similar methodology are presented here. This innovative use of QDAS holds great promise for future nursing informatics research.