On-chip enrichment and analysis of peptide subsets using a maleimide-functionalized fluorous affinity biochip and nanostructure initiator mass spectrometry.

A new nanostructure initiator mass spectrometry (NIMS) methodology is presented that uses the strategy of fluorous-phase immobilization and capture by a maleimide-functionalized affinity tag to selectively enrich peptide subsets containing cysteine residues. This surface-based approach allows complex protein digests to be analyzed. The proposed platform makes use of a chemically unmodified porous silicon (pSi)-based NIMS chip. Unlike matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS), the approach described in this paper does not require analytes to be incorporated or cocrystallized with an initiator. The mass spectra generated by the approach in this work are characterized by low background noise and, therefore, high analyte detection sensitivity. Experiments were also conducted that show the potential the approach described in this work has for generating simplified mass spectra for MS/MS analyses.