On silico peptide microarrays for high-resolution mapping of antibody epitopes and diverse protein-protein interactions

Jordan V. Price, Stephanie Tangsombatvisit, Guangyu Xu, Jiangtao Yu, Dan Levy, Emily C. Baechler, Or Gozani, Madoo Varma, Paul J. Utz, Chih Long Liu

Research output: Contribution to journalArticlepeer-review

91 Scopus citations


We developed a new, silicon-based peptide array for a broad range of biological applications, including potential development as a real-time point-of-care platform. We used photolithography on silicon wafers to synthesize microarrays (Intel arrays) that contained every possible overlapping peptide within a linear protein sequence covering the N-terminal tail of human histone H2B. These arrays also included peptides with acetylated and methylated lysine residues, reflecting post-translational modifications of H2B. We defined minimum binding epitopes for commercial antibodies recognizing the modified and unmodified H2B peptides. We further found that this platform is suitable for the highly sensitive characterization of methyltransferases and kinase substrates. The Intel arrays also revealed specific H2B epitopes that are recognized by autoantibodies in individuals with systemic lupus erythematosus who have elevated disease severity. By combining emerging nonfluorescence-based detection methods with an underlying integrated circuit, we are now poised to create a truly transformative proteomics platform with applications in bioscience, drug development and clinical diagnostics.

Original languageEnglish (US)
Pages (from-to)1434-1440
Number of pages7
JournalNature Medicine
Issue number9
StatePublished - Sep 2012

Bibliographical note

Funding Information:
We thank H. Lee, J. Zhu and the other members of the peptide array team at Biomedical Life Science at Digital Health Intel for development of the early peptide array process and G. Credo for help with the Online Methods section of the manuscript. We thank D. Hall, K.C. Garcia, S. Sidhu, J. Haddon, J. Jarrell and other members of our laboratories for helpful discussion. J.V.P. was funded by a US National Science Foundation Graduate Research Fellowship (NSF GRFP) and is supported by the Stanford Genome Training Program (SGTP; US National Institutes of Health (NIH), US National Human Genome Research Institute). D.L. is supported by the European Molecular Biology Organization, the Human Frontier Science Program and the Machiah Foundation. O.G. is a recipient of an Ellison Senior Scholar Award and is funded by a grant from the NIH (R01 GM079641). P.J.U. is the recipient of a Donald E. and Delia B. Baxter Foundation Career Development Award and is supported by National Heart, Lung, and Blood Institute (NHLBI) Proteomics contract HHSN288201000034C, Proteomics of Inflammatory Immunity and Pulmonary Arterial Hypertension; grants from the NIH (5 U19-AI082719, 5 U19-AI050864, 5 U19-AI056363, 1 U19 AI090019 and 4 U19 AI090019); Canadian Institutes of Health Research (2 OR-92141); Alliance for Lupus Research (grant number 21858); a gift from the Ben May Trust and a gift from the Floren Family Trust. The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement number 261382. C.L.L. is a recipient of an NIH National Research Service Award Fellowship (5 F32 AI-080086-02).


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