Focus on Cancer Proteomics

Abstract

Motivated by the ever increasing demands for improved analytical and computational capabilities in support of proteomic research, technology has rocketed forward. As an example, high-end mass spectrometry touts a competitive half-life on par with Moore's law in the computer industry. Every few years we can expect significant technical improvement in the tools applied to this rapidly growing field. Although it is often easy to become enamored by these technological advances, it is critical that these do not distract from the equally important activities related to developing robust applications to maximize the biomedical impact of these developmental cycles. The field of Cancer Proteomics is ultimately dependent upon developing, standardizing and applying novel technologies to difficult, often-elusive, clinical questions. Many of the assumptions used to develop improved technology do not resonate with the realities of experimentation with clinical samples or complex models of disease. The objective of this Focus Issue is to highlight successful efforts in the application of novel technologies for cancer proteomic studies. Included in this issue are four full-length articles and three technical notes that span a variety of technology application. Morrissey et al. describe a robust approach for the application of label-free LC-MS/MS-based quantitation of serum for the discovery of candidate protein biomarkers of prostate cancer. The design is toward a pipeline from discovery within a clinical trial cohort to a testable MRM-based assay. Chao et al., recognizing the important role of the immune response in both disease development and treatment, describe an array-based approach for profiling patient autoimmune responses. They detail an application of this technology to uncover an immunosuppressive effect of hormone therapy in breast cancer patients. Longuespee et al. present a study that employs MALDI MS imaging to uncover molecular events that potentially drive histopathologic etiology of serous ovarian cancer. In an attempt to address the issue of low abundance tumor specific proteins, researchers may be able to resort to the analysis of cell models. In this issue, Marimuthu et al. examine the secretome of gastric tumor cell lines utilizing SILAC-based quantitation. Similarly, Roper et al. employed azido sugar metabolic labeling to assist in the capture and quantitative analysis of the secretome in a prostate cancer stromal cell model. Our series concludes with two articles describing technological improvements in the application of protein arrays. Festa et al. describe the application of 1-Step human-coupled in vitro transcription/translation for the efficient expression of target proteins in a mammalian IVT system. Wang et al., from the same group, describe a novel approach to achieve expression and arraying of denatured proteins specifically targeted at the identification of disease specific autoantibodies. Our sampling of advances in technology application, although somewhat diverse, is focused on overcoming barriers common to the field of clinical proteomics. We thank the authors for their generous commitment of time and energy to make this Focus Issue a success!