Mapping of international protein index to affymetrix probe-set identifier for correlating genomics and proteomics expression profiles in multiple myeloma

Affymetrix microarrays are widely used in genomics studies. Likewise, International Protein Index (IPI) hosted at European Bioinformatics Institute (EBI) and UniProtKB protein databases are commonly used in proteomics studies, more so in mass spectrometry based proteomics. However, a complete mapping from these protein identifiers (Ids) to Affymetrix Ids is currently unavailable resulting in loss of critical information while inter-converting between proteomics and genomics datasets. This in turn has the potential to result in inaccurate downstream data analysis. Our objective is to maximize the mapping of IPI protein Ids to their corresponding Affymetrix probe set Id(s) to enable correlation of proteomics and genomics expression datasets. Thus, we have created mapping tables to link IPI Ids to their corresponding Affymetrix probe-set identifier(s). These mappings were obtained by parsing publicly available standard mapping annotations for IPI, Affymetrix, and Ensembl in order to establish a link between IPI and Affymetrix Id(s) using all possible identifier types that are common to both respective databases. A web-based tool, 'IPI2Affy' was created to enable querying and retrieval of these Id conversions (http://binfapp. host.ualr.edu/~shweta/ipi2affy.html).