Hi,

I think a bit of additional information is required to be able to answer your question.

What samples would you like to analyze (what is the matrix, what is the approximate protein concentration, etc.)?

Have you purified a set of proteins that you expect to be involved in the synthesis of nanoparticles (what kind of nanoparticles are you referring to, BTW?)?

A standard means to identify a protein is to digest it, for example with trypsin, and then generate mass and fragmentation data of the resulting peptides, by means of mass spectrometry.

These data can then be compared to that available in databases to enable identification of your protein(s) of interest.

MALDI can be used if you have a pure, or simple mixture of, protein(s), otherwise it is advised to use liquid chromatography coupled to ESI-MS, to first separate generated peptides before mass and fragmentation analysis.

Of course, in addition to a mass spectrometer, access to a database and search engine (software) is also of importance for successful identification of a (set of) protein(s).

Hope this helps!