Suggestions for a protein species identifier system.
ABSTRACT Protein variants, which vary in their exact chemical composition, are termed protein species independently if they are coded by one gene or by a paralogous or orhtologous gene or alleles of that gene. The term protein species covers splicing variants, truncated proteins and posttranslational modified proteins and is defined chemically in contrast to the term isoform, which is defined genetically. The importance of the knowledge of the exact chemical composition of a protein species is given by the relationship between its composition and its function. Since several centuries it is already known that posttranslational modifications such as phosphorylation critically determine the activity status of enzymes. Proteolytic truncations can activate proteases, peptide hormones or receptors. However, despite of this knowledge, the relationship of the exact chemical composition of a protein and its function is not yet fully taken into account in many investigations of proteins. In many of the current proteomics studies protein identification is based on sequence coverage significantly lower than 100 %. Posttranslational modifications are more or less ignored. A second drawback concerning the comprehensive description of protein species derives from the absence of an identifier system, which describes its exact chemical composition. Therefore up to now we have to deal with a huge ambiguity concerning the identity of a protein and its function. In the past functions were assigned to genes, implicating that the full information for the function is encoded in the DNA sequence. Now it becomes clear that different modification and even different combinations result in different protein species with different functions. An identifier system for protein species allows assigning a defined function to a defined protein species, which is described by its exact chemical composition. The protein species identifier system was introduced in 2009 by Schlüter et al. and is extended here.