A method for quantitating protein expression using LC/MS of whole proteins is described. This method is based on the fact that some proteins present in cells are abundant universal proteins whose expression levels exhibit little variation. This method demonstrates that these coextracted proteins can be used as internal standards to which the other proteins in the sample can be compared. By comparing the intensities of a selected protein to marker proteins, or internal standards, a relative ratio is obtained. This ratio can then be used to determine the relative amount of protein expression between cellular extracts. The validity of this approach is described for a standard protein mixture, as well as, E. coli cells that were known to differentially express green fluorescent protein.
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