Proteomics is transforming our understanding of biology. While genomics provides the blueprint, proteomics reveals the dynamic molecular processes that underpin health and disease, offering insights into biological activity that DNA alone cannot capture.
Advances in mass spectrometry, affinity-based technologies, protein sequencing and artificial intelligence are accelerating discovery across biomarker research, drug development and precision medicine.
At the same time, the pace of innovation has made proteomics an increasingly complex field to navigate.
We are pleased to introduce the second edition of The Proteomics Playbook—a free, 90-page intelligence-led report developed with guidance from leading experts across academia, healthcare and industry.
Rather than simply summarising the published literature, this playbook combines practical experience with independent analysis of today’s proteomics technology landscape. Alongside expert interviews and commentary, you’ll find comprehensive overviews of commercially available platforms, emerging technologies and the experimental considerations that researchers face when selecting methods, designing workflows and planning future investment.
Whether you’re already working with proteomics or exploring how these technologies could strengthen your research, this report has been designed to help you make more informed scientific and strategic decisions.
Highlights from this edition include:
- Expert interviews and discussions with researchers developing and applying proteomics technologies across academia, healthcare and industry, sharing practical lessons that extend beyond the published literature.
- Independent overviews of commercially available proteomics platforms alongside emerging technologies that are likely to shape the future of the field.
- Guidance covering the latest advances in sample preparation, mass spectrometry, affinity-based proteomics, protein sequencing and approaches for measuring the dynamic nature of proteins.
- An exploration of how artificial intelligence is transforming proteomics, from protein structure prediction to analysing increasingly complex datasets and extracting new biological insight.
- A look at how proteogenomics and precision medicine are accelerating biomarker discovery, translational research and therapeutic development.
Thank you to our contributors
This edition has been developed with the support and expertise of leading researchers from around the world. We are extremely grateful to the following contributors for generously sharing their knowledge and experience:
- Michael Snyder, Professor of Genetics, Stanford University
- Martin Rutter, Deputy Chief Scientist, UK Biobank
- Parag Mallick, Associate Professor, Stanford University
- Claire Eyers, Professor of Biological Mass Spectrometry, University of Liverpool
- Stacy Malaker, Associate Professor of Chemistry, Yale University
- Claudia Ctortecka, CLP Translational Proteomics Fellow, Northwestern University
- Christopher D. Whelan, Founder, UK Biobank Pharma Proteomics Project; Founder, Ignition Scientific
- Mine Koprulu, Postdoctoral Researcher, Precision Healthcare University Research Institute (PHURI)
- Ateequllah Hayat, Lecturer in Drug Development, St George’s School of Health and Medical Sciences
- Silvia Surinova, Proteomics Team Lead, University College London
- Karin Rodland, Director, Precision Medicine Innovation CoLaboratory, Pacific Northwest National Laboratory
- Satoshi Yoshiji, Associate Professor, McGill University
- Siqi Sun, Associate Professor, Fudan University
- Akos Vegvari, Senior Research Specialist, Karolinska Institutet
- Simeon Mihaylov, Senior Postdoctoral Researcher, The Francis Crick Institute
- Jack Houghton, Postdoctoral Researcher, Imperial College London
Chapter Overview
Chapter 1: Protein purification and sample preparation
Effective proteomics begins with robust sample preparation. This chapter explores key considerations for protein purification, cell lysis, denaturation, digestion and clean-up, alongside automation platforms, integrated workflows and commercial solutions designed to improve reproducibility, throughput and data quality.
Chapter 2: Advances in mass spectrometry-based proteomics
Mass spectrometry continues to evolve rapidly, delivering greater sensitivity, throughput and analytical capability. Discover the latest commercial developments, advances in single-cell and spatial proteomics, improvements in detecting post-translational modifications, and expert perspectives on the opportunities and limitations of today’s mass spectrometry platforms.
Chapter 3: Advances in affinity-based proteomics and protein sequencing
Affinity-based technologies are enabling the measurement of thousands of proteins simultaneously, opening new possibilities for high-throughput studies and large population cohorts. This chapter also explores the emergence of next-generation protein sequencing technologies, including single-molecule approaches, nanopore-based methods and other innovations that could reshape the future of proteomics.
Chapter 4: Dynamic proteomics
Proteins are dynamic molecules, and understanding their interactions, localisation, modifications and secretion is essential for capturing biological complexity. Explore technologies for studying the interactome, secretome and post-translational modifications, together with emerging approaches for measuring protein dynamics across diverse biological systems.
Chapter 5: Proteogenomics and precision medicine
Combining proteomics with genomics provides a richer understanding of disease biology than either technology alone. This chapter explores applications in biomarker discovery, drug development, immunopeptidomics, neoantigen identification and precision medicine, demonstrating how integrated molecular data is advancing translational research.
Chapter 6: How AI is shaping proteomics
Artificial intelligence is rapidly becoming embedded throughout the proteomics workflow. From structural prediction and peptide identification to interpreting complex datasets and generating biological insight, discover how AI is accelerating discovery while also exploring the practical considerations surrounding its implementation.
Chapter 7: Translating proteomics to the clinic
Clinical proteomics is moving from promise towards practice. This chapter examines the opportunities and challenges involved in translating proteomics into routine healthcare, including biomarker validation, proteomic risk scores, standardisation, regulation and the pathway towards clinical implementation.
We hope you enjoy reading the second edition of The Proteomics Playbook and that it becomes a valuable resource for your research.
