Targeted protein characterization by mass spectrometry

A method for characterizing proteins of target host cells, comprising the steps of:

• providing a library of measured reference mass spectra of proteins of reference host cells wherein each reference mass spectrum comprises mass signals of digest peptides which are generated by an enzymatic digest of multiple proteins of one type of reference host cells and are extracted by affinity capture using multiple affinity agents after the enzymatic digest;
• enzymatically digesting the proteins of the target host cells under the same conditions used for the proteins of the reference host cells and then extracting the digest peptides by affinity capture using the multiple affinity agents;
• acquiring a mass spectrum for the extracted digest peptides of the target host cells;
• determining similarity scores of the intensity pattern of the mass spectrum and the reference mass spectra;
• and
• characterizing the target host cells by assigning the proteins of the target host cells to a type of reference host cell having a reference spectrum with a similarity score above a predetermined threshold.