In principle, you should be able to quantify unconjugated peptide in the wash batch and you will know how much has been used for metallic nanoparticles conjugates.

If there is a tryptophan residues in your peptide, you can measure UV absorption at 280 nm and calculate the amount of peptide based on Beer-Lambert law and extinction coefficient of your peptide.

Here is a extinction coefficient calculator:

https://web.expasy.org/protparam/

If not, there are several colorimetric or fluorescent quantitative peptide assays can be used.

Take a look here:

https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-mass-spectrometry-analysis/sample-prep-mass-spectrometry/protein-peptide-quantitation-assays-mass-spectrometry.html

From my reading about antibody-drug conjugation (Antibody = Protein). i found they are calculating what is called the Drug-to-Antibody Ratio (DAR) which is based on the mass spectra of the antibody alone and the conjugated one. DAR (Drug-Antibody Ratio) is calculated by dividing the difference between the masses of the conjugated and unconjugated antibodies by the anticipated mass change upon conjugating one mole of the corresponding drug. I hope this is useful for you

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