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Updated: Apr 5, 2026
A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
Published on: April 18, 2025
Quantitative Proteomic Analysis of Differentially Expressed Protein Profiles Involved in Pancreatic Ductal
Kung-Kai Kuo1, Chao-Jen Kuo, Chiang-Yen Chiu
1From the *Division of Hepatobiliary Surgery, Department of Surgery, Kaohsiung Medical University Hospital, †Center for Stem Cell Research, ‡Graduate Institute of Medicine, College of Medicine, §Department of Biotechnology, College of Life Science, and ∥Center for Research Resources and Development, Kaohsiung Medical University, Kaohsiung, Taiwan; ¶Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, NY; #Department of Pathology, Kaohsiung Municipal Hiao Kang Hospital; **Department of Radiology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University; ††Department of Medical Imaging, Kaohsiung Medical University Hospital; ‡‡Department of Genome Medicine, College of Medicine, Kaohsiung Medical University; §§Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung; ∥∥Institute of Biological Chemistry, Academia Sinica, Taipei; and ¶¶Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.
Objectives:
The aim of this study was to identify differentially expressed proteins among various stages of pancreatic ductal adenocarcinoma (PDAC) by shotgun proteomics using nano-liquid chromatography coupled tandem mass spectrometry and stable isotope dimethyl labeling.
Methods:
Differentially expressed proteins were identified and compared based on the mass spectral differences of their isotope-labeled peptide fragments generated from protease digestion.
Results:
Our quantitative proteomic analysis of the differentially expressed proteins with stable isotope (deuterium/hydrogen ratio, ≥ 2) identified a total of 353 proteins, with at least 5 protein biomarker proteins that were significantly differentially expressed between cancer and normal mice by at least a 2-fold alteration. These 5 protein biomarker candidates include α-enolase, α-catenin, 14-3-3 β, VDAC1, and calmodulin with high confidence levels. The expression levels were also found to be in agreement with those examined by Western blot and histochemical staining.
Conclusions:
The systematic decrease or increase of these identified marker proteins may potentially reflect the morphological aberrations and diseased stages of pancreas carcinoma throughout progressive developments leading to PDAC. The results would form a firm foundation for future work concerning validation and clinical translation of some identified biomarkers into targeted diagnosis and therapy for various stages of PDAC.
