The mouse is the premier genetic model organism for the study of disease and development. We describe the establishment of a mouse T helper cell type 1 (T H 1) protein expression library that provides direct access to thousands of recombinant mouse proteins, in particular those associated with immune responses. The advantage of a system based on the combination of large cDNA expression libraries with microarray technology is the direct connection of the DNA sequence information from a particular clone to its recombinant, expressed protein. We have generated a mouse T H 1 expression cDNA library and used protein arrays of this library to characterize the specificity and cross-reactivity of antibodies. Additionally, we have profiled the autoantibody repertoire in serum of a mouse model for systemic lupus erythematosus on these protein arrays and validated the putative autoantigens on highly sensitive protein microarrays. D 2004 Elsevier Inc. All rights reserved.Keywords: T H 1; cDNA expression library; Automation; Mouse; High-density protein arrays; Microarrays; Protein chips; Serum profiling; SLE; Autoantibody The mouse is the premier genetic model organism for the study of disease and development [1]. The final sequencing of the entire mouse genome [2] will greatly increase the advantages associated with mouse models. One of the next steps in expanding the usefulness of mouse models will be to make available tens of thousands of mouse proteins for large-scale high-throughput analyses, e.g., the study of antibody-protein, protein-protein, and peptide-protein interactions and enzyme activities and the characterization of antibody specificity. Such high-throughput studies are greatly simplified by protein microarray technology, whereby thousands of biomolecules are immobilized at high density onto chemically modified surfaces. The advantages of a system based on the combination of large cDNA expression libraries with microarray technology are the direct accessibility of the expressed recombinant proteins and of the DNA sequence information from a particular clone and the ability to re-array the recombinant proteins from selected clones to generate a new microarray for the creation of high-density protein arrays on glass chips [3]. For the generation of protein biochips high-throughput subcloning of open reading frames from the genome of humans, Saccharomyces cerevisiae, Arabidopsis thaliana, and Caenorhabditis elegans have been described [34][35][36][37][38][39]. Such recombination-based cloning approaches are strongly dependent on the progress in genome sequencing projects and the annotation of those sequences [40,37]. This means that previously uncharacterized proteins will be absent,