Finding one's way in proteomics: a protein species nomenclature

The number of publications in the field of proteomics has increased dramatically over the last decade. The driving force behind this development has been the hope of gaining additional insights into the functioning of a cell or of a complete organism by identification and quantification of proteins in different biological states such as disease and health, wild type and mutant, baseline and perturbed state, among others. The dynamics and the influence of post-translational protein modifications were mostly ignored in the course of development of the basic technologies during these years. The focus on technology has nonetheless resulted in dramatic improvements in mass spectrometry and in coupling MS with two-dimensional electrophoresis and liquid chromatography. The improvements and results gained over time in proteomics research have shown that the behaviour and variability of proteins are more complex than had ever been imagined. The fact that the same protein was found at several different spots on 2-dimensional electrophoresis gels made it necessary to define a new term for these different forms of a single protein: protein species [1,2]. Each additional modification and each new combination of modifications represents an additional protein species of that single protein. Though the term protein species had been used earlier in the literature [3,4], it was not clearly defined and used more in the sense of a protein complex consisting of several subunits [3] or to differentiate between different proteins (e.g. catalase and actin were two different protein species) [4]. According to the IUPAC rules [5] the term "isoform" is to be used for genetic variations such as allelic forms. Therefore, it was necessary to find a term for any chemical modification and any combination of chemical modifications. The term "protein species" has been defined by Jungblut et al. at the chemical, molecular level [1,2]. According to this definition, isoforms represent different protein