In this study, we report new results of in situ study of 5 nm goat anti-mouse IgG gold nanoparticles in a novel portable vacuum compatible microfluidic device using scanning electron microscope (SEM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The unique feature of the liquid flow cell is that the detection window is open to the vacuum allowing direct probing of the liquid surface. The flow cell is composed of a silicon nitride (SiN) membrane and polydimethylsiloxane (PDMS), and it is fully compatible with vacuum operations for surface analysis. The aperture can be drilled through the 100 nm SiN membrane using a focused ion beam. Characteristic signals of the conjugated gold nanoparticles were successfully observed through the aperture by both energy-dispersive X-ray spectroscopy (EDX) in SEM and ToF-SIMS. Comparison was also made among wet samples, dry samples, and liquid sample in the flow cell using SEM/EDX. Stronger gold signal can be observed in our novel portable device by SEM/EDX compared with the wet or dry samples, respectively. Our results indicate that analyses of the nanoparticle components are better made in their native liquid environment. This is made possible using our unique microfluidic flow cell. Copyright © 2013 John Wiley & Sons, Ltd.