The benefits of the present proteomic approaches for the life science community are limited by 3 major problems. 1. The identification of proteins, regardless whether the peptide mass fingerprint or the shot-gun approach is used, usually is based on an incomplete set of peptides leaving large parts of the full amino acid sequence and other structural details of the original protein species in the dark; 2. Missing validation of many of the identified proteins by orthogonal biological experiments

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... thus risking false positive results; 3. Missing standardization in nomenclature. In sum these problems may hinder progress in life science projects employing proteomic strategies and may be especially risky for system biology approaches since the ambiguities resulting from the above mentioned problems may cause wrong models. It is recommended to guide future proteome analytical investigations by a hypothesis and to focus to a smaller number of proteins which should ideally be analyzed in detail covering 100 % sequence coverage as well as all posttranslational modifications and will allow validation by additional biological experiments.