In situ molecular imaging of protein films adsorbed on a solid surface in water was realized by using a vacuum compatible microfluidic interface and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Amino acid fragments from such hydrated protein films are observed and identified in the positive ion mode and the results are in agreement with reported works on dry protein films. Moreover, water clusters from the hydrated protein films have been observed and identified in both the positive and negative ion mode for a series protein films. Thus, the detailed composition of amino acids and water molecules in the hydrated protein films can be characterized, and the protein water microstructures can be revealed by the distinct three-dimensional spatial distribution reconstructed from in situ liquid ToF-SIMS molecular imaging. Furthermore, spectral principal component analysis of amino acid fragment peaks and water cluster peaks provides unique insights into the water cluster distribution, hydrophilicity, and hydrophobicity of hydrated adsorbed protein films in water. Hydration is crucial to keep the conformation and biological activity of proteins 1,2. It is well-known that water molecules around proteins have properties quite distinct from those in the aqueous bulk phase 3,4. As a representative form of hydrated proteins, the hydrated protein films consist of a mixed layer of protein and water molecules 5,6. Thus, the revelation of the composition and structure of hydrated protein films, especially for the distribution of water molecules within them, is an effective way to understand the hydration mechanism of proteins. Adsorbed protein films on a solid surface have been widely studied because of their unique feature in cell adhesion, which has multiple applications in biology and medicine, such as cell culture 7 and implantable device manufacture 8. The composition and structure of adsorbed hydrated protein films are usually evaluated by analyzing their dry samples due to the technical and instrumental limitations to study the solid-liquid interface using surface sensitive techniques that are largely constrained because of vacuum conditions 9,10. The orientation of the adsorbed protein molecules is of great interest 9,10. However, the dry protein film is rather different from the hydrated protein film in its natural state. While dry sample surface analysis is useful to provide ensemble measurements of the chemical composition, thickness, and possibly orientation, they do not necessarily reflect the composition and structure of hydrated protein films in water. More importantly, the water microenvironment surrounding the protein and water molecules associated with the protein structure are lost in dry sample analysis. Actually, as far as we know, few experimental techniques can be used to analyze the water microenvironment surrounding the protein molecules, and most understandings in this field have been from computational efforts 1,11,12. Therefore, direct molecular evidence is of great importance to verify t...