Data processing, validation, standardizations, and protein quantification are few of the brewing issues surrounding the field of human genome and proteomics.  There is a dire need for standardized analysis methods and a workflow focus.  Various types of software warehousing and analysis methods should help address the different issues in a flexible manner.  Creating a central database would provide a good solution to compare experiments to one another and to extract knowledge based on past experiments.  One such database and search engine has been created for comparing peptide identification from various experiments (ESI and MALDI) to produce an integrated result showing you the possible proteins.  It can be expected that in the near future all protein identifications will come with a statistical significance so everyone can judge the validity of the information.  However, making this method standardized and reproducible will be key.  However, much like in the genomics arena, the issue in bioinformatics will be the opulence of raw data and the need for fast multi-resolution  visualization tools.