The epidermal growth factor receptor (EGFR) is highly expressed in a variety of tumors, and is therefore an important biomarker for cancer diagnosis and a target for cancer therapy. We have developed a novel peptide-based immuno tandem mass spectrometry (iMALDI) diagnostic assay for highly sensitive, highly specific, and quantitative analysis of EGFR, which we have applied to the detection of the EGFR peptide in three cell lines and in a tumor biopsy sample. This assay is capable of detecting the EGFR target peptide bound to the antibody beads at attomole levels. The ability to directly obtain amino acid sequence data by MS/MS on any affinity-captured peptides provides specificity to this diagnostic technique. This avoids the problem of “false positives” which can result from the nonspecific binding that can occur with any affinity-based technique. The addition of stable-labeled versions of the target peptide (synthesized from stable-isotope coded amino acids) as internal standards allows absolute quantitation of the target protein.