Methyl- and carboxy-terminated self-assembled monolayers (SAMs) were custom-patterned on porous gold substrates with equipment commonly used to print protein arrays, without complex surface chemistry protocols. Proteins were covalently immobilized on hydrophilic carboxy-terminated SAM spots, while the remainder of the surface was superhydrophobic due to the roughened gold surface and the methyl-terminated SAM. The resistance of these patterns to biofouling and the effective containment of MALDI matrix solution within the hydrophilic spot made these surfaces amenable to analyzing protein-peptide binding with mass spectrometry. A model system of the affinity peptides HA, cmyc, and V5 and their corresponding antibodies was used to demonstrate the utility of the patterned porous gold. Mass spectrometry (MS) and tandem mass spectrometry (MS/MS) matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectra and images obtained reflected the effective capture of the affinity peptides directly from spiked bovine plasma.