Affinity profiling using the peptide microarray technology: a case study.
Little about the reliability of measurements obtained using synthetic peptide microarrays is known. We report results from a study on the quantitative reliability of microarrays manufactured by robot-supported immobilization of presynthesized peptides for different microarray platforms. Technological precision is assessed for inter- and intra-device readout comparisons. Correlations between measured signals and known dissociation constants using a phenomenological model derived from the mass action law are discussed. Special emphasis is on discussing the pitfalls of high-throughput affinity measurements. We show that the quantitative determination of binding affinities is prone to be biased toward a mean affinity of around 10(-7)M, while the classification of peptides into either "binders" or "nonbinders" provides very high prediction accuracy. The experimental requirements needed to obtain reliable binding affinity predictions are discussed.
Tapia
Victor
V
Institute for Theoretical Biology, Humboldt University, Invalidenstrasse 43, 10115 Berlin, Germany.
Bongartz
Juliane
J
Schutkowski
Mike
M
Bruni
Nicole
N
Weiser
Armin
A
Ay
Bernhard
B
Volkmer
Rudolf
R
Or-Guil
Michal
M
D000911:Antibodies, Monoclonal / Q000737:chemistry*; D002482:Cellulose / Q000737:chemistry; D016655:HIV Core Protein p24 / Q000276:immunology*; D006801:Humans; D046228:Microarray Analysis; D010452:Peptide Biosynthesis; D010446:Peptide Fragments / Q000737:chemistry*; D040081:Protein Array Analysis; D011485:Protein Binding; D020349:Surface Plasmon Resonance
D000911:Antibodies, Monoclonal; D016655:HIV Core Protein p24; D010446:Peptide Fragments; D002482:Cellulose