This paper introduces four different notions of correctness to be used when measuring the performance of protein name taggers, each of which reflects certain characteristics of the tagger under evaluation. The discussion regarding the different notions is centered around the evaluation of two protein name taggers; Yapex, developed by the authors, and KeX developed by Fukuda et al (1998). For the purpose of illustrating the difference between the ways of evaluation, both taggers are applied to a corpus of 101 MEDLINE abstracts in which all occurrences of protein names have been marked up by domain experts