[Frontiers in Bioscience 14, 3292-3303, January 1, 2009]

Proteomics strategies for target identification and biomarker discovery in cancer

Uros Rajcevic1, Simone P. Niclou1 and Connie R. Jimenez2

1Norlux Neuro-Oncology Laboratory, CRP-Sante, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg, 2OncoProteomics Laboratory, VUmc-Cancer Center Amsterdam, VU University Medical Center, De Boelelaan 1081, Amsterdam, The Netherlands

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. General considerations in sample selection for cancer proteomics
4. Two dimensional gel-based proteomics
5. LC-MS/MS-based proteomics
6. Quantitative MS and LC-MS
6.1. Sample labeling approaches 6.1.1. Stable isotope labeling of amino acids in cell culture (SILAC)
6.1.2. Heavy water labeling
6.1.3. Isotope-coded affinity tags (ICAT)
6.1.4. Isobaric Tags for Relative and Absolute Quantification of peptides (iTRAQ)
6.2. Label-free quantitation in LC MS-based proteomics
7. Biofluid peptide profiling by mass spectrometry after high-throughput single step peptide capture
8. Biomarker discovery in biofluids
9. Target identification for anti-angiogenic therapy
10. Concluding remarks
11. Acknowledgements
12. References

1. ABSTRACT

The revolution in genomics and proteomics has produced complex technologies enabling an insight into the functional effectors of cellular processes. In oncology these technologies lead to the identification of biological markers which may provide the starting point for the development and identification of diagnostic tests and therapeutic targets. To identify and validate reliable tumor markers within the proteome, it is necessary, prior to tandem mass spectrometry, to reduce sample complexity. This can be done by robust fractionation and separation techniques. This review addresses the discovery stage of onco-proteomics - the strategies for target identification and biomarker discovery in solid tumors and biofluids. The overview includes different proteomic methods, from gel-based to liquid chromatography (LC)-based separations of proteins/peptides, and the corresponding detection by mass spectrometry. The quantitative methods in mass spectrometry include techniques based on stable isotope labeling of proteins/peptides and label-free methods. A particular emphasis is given to proteomics-based biomarker discovery in biofluids (e.g. plasma, urine, secretome, cerebrospinal fluid) and target identification in tissue for anti-angiogenic therapies.