Targeted proteomics of solid cancers: from quantification of known biomarkers towards reading the digital proteome maps

Abstract

The concept of personalized medicine includes novel protein biomarkers that are expected to improve the early detection, diagnosis and therapy monitoring of malignant diseases. Tissues, biofluids, cell lines and xenograft models are the common sources of biomarker candidates that require verification of clinical value in independent patient cohorts. Targeted proteomics – based on selected reaction monitoring, or data extraction from data-independent acquisition based digital maps – now represents a promising mass spectrometry alternative to immunochemical methods. To date, it has been successfully used in a high number of studies answering clinical questions on solid malignancies: breast, colorectal, prostate, ovarian, endometrial, pancreatic, hepatocellular, lung, bladder and others. It plays an important role in functional proteomic experiments that include studying the role of post-translational modifications in cancer progression. This review summarizes verified biomarker candidates successfully quantified by targeted proteomics in this field and directs the readers who plan to design their own hypothesis-driven experiments to appropriate sources of methods and knowledge.

Keywords:

• biomarker
• bodily fluids
• cancer
• selected reaction monitoring
• data independent acquisition
• tissue
• verification

Acknowledgements

We thank Dr. Peter Grell (Masaryk Memorial Cancer Institute), for his comments on the clinical utility of the current biomarkers and Eva Michalová (Masaryk Memorial Cancer Institute) for critical reading of the manuscript.