The role of proteomics in the multiplexed analysis of gene alterations in human cancer

ABSTRACT

Introduction

Proteomics has played a pivotal role in identifying proteins perturbed in disease conditions when compared with healthy samples. Study of dysregulated proteins aids in identifying diagnostic markers and potential therapeutic targets. Cancer is an outcome of interplay of several such disarrayed proteins and molecular pathways which perturb cellular homeostasis, resulting in transformation. In this review, we discuss various facets of proteomic approaches, including tools and technological advancements, aiding in understanding differentially expressed molecules and signaling mechanisms.

Areas covered

In this review, we have taken the approach of documenting the different methods of proteomic studies, ranging from labeling techniques, data analysis methods, and the nature of molecule detected. We summarize each technique and provide a glimpse of cancer research carried out using them, highlighting the advantages and drawbacks in comparison with others. Literature search using online resources, such as PubMed and Google Scholar were carried out for this approach.

Expert opinion

Technological advancements in proteomics studies have come a long way from the study of two-dimensional mapping of proteins separated on gels in the early 1970s. Higher precision in molecular identification and quantification (high throughput), and greater number of samples analyzed have been the focus of researchers.

KEYWORDS:

• Cancer proteomics
• iTRAQ
• mass spectrometry
• MRM/SRM
• SILAC
• phosphoproteomics
• proteogenomics
• proteomics
• TMT

Article highlights

• Introduction and summary of different methods of protein quantification, including label-free and labeling techniques used in proteomics approach applicable in cancer research, such as stable-isotope labelling by amino acids in cell culture (SILAC), tandem mass tags (TMT), and Isobaric tag for relative and absolute quantitation (iTRAQ)

• Summary of cancer research based on the nature of molecules identified and the technical assessment carried out using those approaches, such as global proteomics, phosphoproteomics, and glycoproteomics

• Future highlights and expert opinion on how technological advancements can lead to higher precision in molecular identification and allow for more samples to be analyzed in tandem

Declaration of Interests

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.