Nature Biotechnology
21, 1509 - 1512 (2003)
Published online: 9 November 2003; | doi:10.1038/nbt910
Analyzing antibody specificity with whole proteome microarraysGregory A Michaud1, Michael Salcius1, Fang Zhou1, Rhonda Bangham1, Jaclyn Bonin1, Hong Guo1, Michael Snyder2, Paul F Predki1
& Barry I Schweitzer11
Protometrix, 688 East Main Street, Branford, Connecticut 06405, USA. 2
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
Correspondence should be addressed to Barry I Schweitzer barry.schweitzer@protometrix.comAlthough approximately 10,000 antibodies are available from commercial sources, antibody reagents are still unavailable for most proteins1. Furthermore, new applications such as antibody arrays2,
3,
4,
5 and monoclonal antibody therapeutics6,
7 have increased the demand for more specific antibodies to reduce cross-reactivity and side effects. An array containing every protein for the relevant organism represents the ideal format for an assay to test antibody specificity, because it allows the simultaneous screening of thousands of proteins for possible cross-reactivity. As an initial test of this approach, we screened 11 polyclonal and monoclonal antibodies to  5,000 different yeast proteins deposited on a glass slide and found that, in addition to recognizing their cognate proteins, the antibodies cross-reacted with other yeast proteins to varying degrees. Some of the interactions of the antibodies with noncognate proteins could be deduced by alignment of the primary amino acid sequences of the antigens and cross-reactive proteins; however, these interactions could not be predicted a priori. Our findings show that proteome array technology has potential to improve antibody design and selection for applications in both medicine and research.
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