Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells

ABSTRACT

Introduction

Many pathologies, including cancer, have been associated with aberrant phosphorylation-mediated signaling networks that drive altered cell proliferation, migration, metabolic regulation, and can lead to systemic inflammation. Phosphoproteomics, the large-scale analysis of protein phosphorylation sites, has emerged as a powerful tool to define signaling network regulation and dysregulation in normal and pathological conditions.

Areas Covered

We provide an overview of methodology for global phosphoproteomics as well as enrichment of specific subsets of the phosphoproteome, including phosphotyrosine and phospho-motif enrichment of kinase substrates. We review quantitative methods, advantages and limitations of different mass spectrometry acquisition formats, and computational approaches to extract biological insight from phosphoproteomics data. Throughout, we discuss various applications and their challenges in implementation.

Expert opinion

Over the past 20 years the field of phosphoproteomics has advanced to enable deep biological and clinical insight through the quantitative analysis of signaling networks. Future areas of development include Clinical Laboratory Improvement Amendments (CLIA)-approved methods for analysis of clinical samples, continued improvements in sensitivity to enable analysis of small numbers of rare cells and tissue microarrays, and computational methods to integrate data resulting from multiple systems-level quantitative analytical methods.

KEYWORDS:

• Cancer
• cellular networks
• kinase activity
• mass spectrometry
• molecular signaling
• phosphoproteomics
• phosphorylation

Article highlights

• Phosphopeptide enrichment methods

• Tyrosine phosphoproteomics

• Phospho-motif enrichment for kinase substrates

• Quantitative phosphoproteomics

• Data acquisition methods for phosphoproteomics

• Computational approaches to identify activated signaling networks

Disclosure Statement

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. Funders of this work had no influence on its content.

Author contribution statement

All authors have substantially contributed to the conception and design of the review article and interpreting the relevant literature. Furthermore, all authors have been involved in writing and revision of the review article.

Additional information

Funding

This manuscript was funded in part by NIH grants U54 CA210180, U01 CA238720, U01 CA215709, and R01 GM139998.