How Reproducible Proteomics Pipelines Are Transforming Protein Analysis

Name: How Reproducible Proteomics Pipelines Are Transforming Protein Analysis
Uploaded: 2026-03-04T00:00:00+00:00
Description: In this interview, Dr. Yasset Perez-Riverol from EMBL-EBI, explores how building reproducible proteomics pipelines with modern workflow engines and software management tools enables data robustness and reusability without sacrificing flexibility.

Video

Published: March 4, 2026

Laura Hemmingham, PhD

speaking with

Yasset Perez-Riverol, PhD

Proteomics is entering a new era where reproducibility, scalability, and data reuse define scientific impact. As datasets grow in both size and complexity, researchers face mounting challenges in tracking data provenance, standardizing workflows, and ensuring long-term accessibility.

In this interview, Dr. Yasset Perez-Riverol, team coordinator of proteomics services at EMBL-EBI, explores how building reproducible proteomics pipelines with modern workflow engines like Nextflow and software management tools like BioContainers and BioConda enables data robustness and reusability without sacrificing flexibility.

Watch this video to discover:

How workflow engines and containers drive true reproducibility in proteomics
Practical strategies for ensuring FAIR proteomics data through data provenance tracking
Why open-source ecosystems accelerate large-scale data reuse

Further resources:

Meet the Author

Laura Hemmingham, PhD

Scientific Content Producer

Laura holds a BSc in Zoology from Queen Mary University of London, an MSc in Palaeoanthropology from UCL, and a PhD in Environmental Sciences from Royal Holloway, University of London. Her academic journey has been fueled by a broad interest in the life sciences and a passion for making complex science accessible to diverse audiences. Before joining Technology Networks in 2025, she gained experience across several areas of science communication, including e-learning, external communications, and science writing. Her work has focused on translating technical research into engaging, understandable content tailored for both specialist and general audiences. As a Scientific Content Producer for custom video content at Technology Networks, Laura is particularly interested in bridging the gap between scientific discovery and public engagement through creative storytelling. Her work aims to support scientific literacy while highlighting the real-world impact of research and innovation.

Interviewing

Yasset Perez-Riverol, PhD

Team Coordinator of Proteomics Services

Yasset Perez-Riverol leads the development of PRIDE at EMBL-EBI, focusing on large-scale proteomics data integration with bioinformatics and machine learning. His work promotes FAIR data principles, standard formats, and tools for reproducible, automated analysis. He supports global projects like Open Targets and ProteomeXchange, and develops open-source tools such as BioContainers and quantms. His goal is to enable AI-driven biology through high-quality, interoperable data.