Pancreatic ductal adenocarcinoma (PDAC) is a major cause of cancer-related 
death, largely due to metastatic disease. To better understand PDAC metastatic 
spread and identify novel therapeutic targets, we analysed the proteome of 
primary tumours and matched lymph node (LN) metastases. As frozen specimens of 
metastatic lesions are scarce, we examined formalin-fixed paraffin-embedded 
(FFPE) tissues. This poses technical challenges because of the cross-linkages 
induced by fixation. Using laser capture microdissection (PALM system), we 
isolated malignant epithelia from seven FFPE primary PDAC tumours and matched LN 
metastases. Following dissection, samples were analysed in duplicate using 
Multidimensional Protein Identification Technology (MudPIT); this resulted in 
the identification of 1504 proteins, 854 of which were common to all samples 
analysed. Comparison of the obtained proteins with data from previous proteomics 
studies on pancreatic tissue, pancreatic juice, serum, and urine resulted in a 
less than 30% overlap, indicating that our study has substantially expanded the 
current database of proteins expressed in this malignancy. Statistical analysis 
further showed that 115/854 proteins (13.5%) were significantly differentially 
expressed (g-value ≥ 3.8). Two proteins, S100P and 14-3-3 sigma, with highly 
significant g-values were confirmed to be significantly differentially expressed 
(S100P: p = 0.05 and 14-3-3 sigma: p < 0.001) in a larger series of 55 cases of 
matched primary PDAC and LN metastases using immunohistochemistry. Thus, laser 
capture microdissection of FFPE tissue coupled with downstream proteomic 
analysis is a valid approach for the investigation of metastatic PDAC. This is 
the first study to establish and compare the protein composition of primary PDAC 
and matched LN metastases, and has resulted in the identification of several 
potential epithelial-specific therapeutic targets, including 14-3-3 sigma and 
S100P.