Detection and identification of peptide and protein modifications

10) A method for quantifying the amount of modified peptide or protein in a sample comprising,

• obtaining a sample containing a target peptide or protein,
• isolating a proteinaceous fraction from the sample containing the target peptide or protein,
• fragmenting proteinaceous material in the proteinaceous fraction to create smaller peptides,
• obtaining a Surface Enhanced Raman Spectrum of one or more of the smaller peptides, and
• comparing one or more peak intensities from the Enhanced Raman Spectrum to a peak intensity from a sample containing a known amount of smaller peptide to determine the amount of peptide from the sample.

18) A method for analyzing a sample comprising:

• providing a substrate having a surface and a plurality of peptides attached to the surface,
• analyzing the surface using Surface Enhanced Raman Spectroscopy,
• contacting the substrate surface with a fluid sample under conditions that allow any components of the sample that are capable of interacting with the plurality of peptides attached to the substrate to react with the peptides attached to the substrate,
• analyzing the surface of the substrate an additional time using Surface Enhanced Raman Spectroscopy, and
• determining a modification state of at least one peptide from the data contained in a Raman spectrum.