This thesis focuses on the application of advanced proteomics and mass spectrometry to pancreatic cancer research and the biology of the Chinese hamster ovary (CHO) cell. Understanding these diverse cell phenotypes is important for the treatment of pancreatic cancer (PDAC) and to improve the efficiency of production of biotherapeutics. Sample preparation, mass spectrometry (using two sensitive, highly accurate and powerful machines which identified thousands of proteins per sample) and bioinformatics analysis are the key components undertaken in this thesis for these studies. Proteomic analysis of PDAC using primary tumours, adjacent-normal tissues, PDX F1 and PDX F2 tumours was carried out. Using subcellular protein enrichment during sample preparation in the PDAC studies allowed the identification of membrane-associated proteins which may have potential as novel targeted therapeutic drugs for PDAC treatment. Bioinformatic analysis in the PDAC study identified proteins overexpressed in the primary tumour and tumour-cell associated proteins in the PDX models. Proteomic analysis of recombinant CHO cells following microRNA engineering of miR-378 and miR-7 which improved culture phenotypes was carried out. Subcellular protein enrichment of the CHO cells enabled deeper proteomic coverage. Bioinformatic analysis in the CHO proteomic studies identified roles for Usp14, the Akt pathway and ribosome biogenesis in improved CHO cell phenotypes related to growth and productivity. The scientific output from this thesis resulted in six publications to date. The proteomic data presented here provide a deeper understanding into the biology of both pancreatic cancer and CHO cells.