Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry.
OBJECTIVE
FFPE tissue is a standard method of specimen preservation for hospital pathology departments. Formalin-fixed paraffin-embedded tissue banks are a resource of histologically characterized specimens for retrospective biomarker investigation. We aim to establish liquid chromatography coupled with tandem mass spectrometry analysis of FFPE pancreatic tissue as a suitable strategy for the study of the pancreas proteome.


METHODS
We investigated the proteomic profile of FFPE pancreatic tissue specimens, using liquid chromatography coupled with tandem mass spectrometry, from 9 archived specimens that were histologically classified as normal (n = 3), chronic pancreatitis (n = 3), and pancreatic cancer (n = 3).


RESULTS
We identified 525 nonredundant proteins from 9 specimens. Implementing our filtering criteria, 78, 15, and 21 proteins were identified exclusively in normal, chronic pancreatitis, and pancreatic cancer specimens, respectively. Several proteins were identified exclusively in specimens with no pancreatic disease: spink 1, retinol dehydrogenase, and common pancreatic enzymes. Similarly, proteins were identified exclusively in chronic pancreatitis specimens: collagen α1 (XIV), filamin A, collagen α3 (VI), and SNC73. Proteins identified exclusively in pancreatic cancer included annexin 4A and fibronectin.


CONCLUSIONS
We report that differentially expressed proteins can be identified among FFPE tissue specimens originating from individuals with different pancreatic histologic findings. The mass spectrometry-based method used herein has the potential to enhance biomarker discovery and chronic pancreatitis research.
Department of Pathology, Harvard Medical School, Boston, MA, USA.
Joao A
JA
Paulo
Linda S
LS
Lee
Peter A
PA
Banks
Hanno
H
Steen
Darwin L
DL
Conwell
D015415:Biomarkers / Q000032:analysis; D001900:Boston; D016022:Case-Control Studies; D002853:Chromatography, Liquid; D019295:Computational Biology; D005404:Fixatives; D005557:Formaldehyde; D006801:Humans; D010179:Pancreas / Q000737:chemistry*; D010190:Pancreatic Neoplasms / Q000737:chemistry*; D050500:Pancreatitis, Chronic / Q000378:metabolism*; D016612:Paraffin Embedding; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry; D016707:Tissue Fixation
D015415:Biomarkers; D005404:Fixatives; D011506:Proteins; D005557:Formaldehyde