Mass spectrometry has long been a cornerstone in proteomics, enabling precise protein analysis and deep biological insights. However, with the growing complexity of biological systems and the need for greater sensitivity, speed, and accuracy, the field continues to face challenges. These include detecting low-abundance proteins, reducing data complexity, and improving workflow efficiency for large-scale studies. Developing advanced systems that can address these issues is essential for pushing the boundaries of what scientists can discover in areas such as biomarker discovery, drug development, and disease research.

Jose Castro-Perez, the vice president of product management at SCIEX, has over two decades of experience in the analytical instrumentation field. With a passion for advancing mass spectrometry technologies, Castro-Perez has played a key role in developing the ZenoTOF 7600+ system, a groundbreaking tool that addresses some of the most pressing challenges in proteomics. Drug Discovery News spoke with Castro-Perez to learn about the innovations behind this technology, its impact on the scientific community, and what the future holds for proteomics research.

Could you tell us a bit about your background and your role at SCIEX?

As the vice president of Product Management, I am responsible for the overall ownership of the global SCIEX product portfolio for capillary electrophoresis, liquid chromatography/mass spectrometry, software ecosystems, and accessories. My journey in analytical instrumentation spans over two decades, and I’ve always been passionate about developing cutting-edge technologies that empower researchers to tackle the most complex biological questions. 

At SCIEX, my role involves guiding innovation, engaging with the scientific community, and ensuring that our solutions like the ZenoTOF 7600+ system meet the evolving needs of scientists in the fields of proteomics, biomarker discovery, and beyond. Together with our global team, we push the boundaries of what is possible in mass spectrometry and proteomics.

What inspired the development of the ZenoTOF 7600+ system? Were there any specific challenges in current mass spectrometry technology that you were hoping to address with this system?

The inspiration for the ZenoTOF 7600+ system came from listening to researchers who were frustrated with limitations in existing systems. One recurring challenge was the trade-off between sensitivity, speed, and precision. Scientists often struggled to detect low-abundance proteins or post-translational modifications (PTMs) with confidence, and workflows were often cumbersome, requiring multiple instruments or steps to complete a dataset.

With the ZenoTOF 7600+ system, we wanted to redefine these limitations. This system integrates our proprietary Zeno trap technology, which boosts sensitivity dramatically, enabling researchers to quantify protein groups at levels that were previously difficult to attain. Additionally, we aimed to streamline workflows by combining high-resolution data acquisition with unparalleled speed, giving researchers a tool that simplifies their processes without compromising on quality. The ZenoTOF 7600+ system is truly a game changer, offering a comprehensive solution for proteomics challenges.

The ZT Scan DIA workflow combines different acquisition modes into one platform. Can you explain how this helps simplify data acquisition in proteomics research, and what benefits it offers in terms of the results researchers get?

The ZT Scan DIA workflow is a breakthrough in simplifying proteomics research. Traditionally, researchers had to choose between data-dependent acquisition (DDA) or data-independent acquisition (DIA), each with its own set of challenges. DDA often misses low-abundance proteins, while DIA can generate overwhelming amounts of data that are difficult to analyze.

With ZT Scan DIA, we have combined the strengths of both approaches into a single workflow. Researchers can now acquire broad, untargeted datasets with the precision of targeted acquisition modes, and they can do it all in one run. This means less time spent setting up experiments and more time focusing on meaningful biological insights.

The benefits are immense. ZT Scan DIA provides more comprehensive coverage of the proteome, higher confidence in quantifying proteins and PTMs, and better reproducibility across experiments. It also simplifies data analysis, enabling even less experienced users to achieve robust results. This workflow empowers researchers to uncover novel insights faster and with greater confidence.

One of the key advancements of the ZenoTOF 7600+ system is its ability to quantify protein groups at sub-nanogram levels. How does this level of sensitivity enhance biomarker analysis?

Sub-nanogram sensitivity is a transformative feature for biomarker analysis. Biomarkers, especially those associated with early-stage diseases, are often present at incredibly low concentrations. Detecting these subtle changes in the proteome can mean the difference between identifying a disease early and missing it altogether.

The ZenoTOF 7600+ system excels at detecting and quantifying these low-abundance proteins with precision, even in complex biological samples. This level of sensitivity allows researchers to uncover potential biomarkers that were previously undetectable, leading to earlier diagnoses, more accurate disease monitoring, and more effective therapeutic interventions. It’s not just about seeing what’s there — it’s about seeing what was once invisible, and that’s a game changer for clinical research and drug development.

How important is speed in proteomics, and how do you think the ZenoTOF 7600+ system will help researchers tackle large-scale studies more efficiently?

Speed is absolutely critical in proteomics, especially as we move toward large-scale studies involving hundreds or thousands of samples. A system’s scanning speed directly impacts how much data can be collected in a given time, and with the ZenoTOF 7600+ system, we’ve set a new benchmark at 640 Hz.

This means researchers can process large datasets much faster without sacrificing data quality. For example, in population-scale studies, where researchers might be analyzing thousands of plasma samples to identify disease biomarkers, the ZenoTOF 7600+ system dramatically shortens the time required to generate results. Faster scanning also ensures that you can capture fleeting molecular details that slower systems might miss, which is crucial for dynamic proteomics experiments. Ultimately, this speed enables researchers to achieve more in less time, accelerating discoveries and increasing efficiency across the board.

The ZenoTOF 7600+ system also stands out for its ability to differentiate isomeric peptides and identify PTMs. How does this level of precision help advance disease research and accelerate drug discovery?

The ability to differentiate isomeric peptides and identify PTMs with high precision is a cornerstone of modern proteomics. PTMs, such as phosphorylation or glycosylation, play key roles in regulating protein function and are often implicated in disease processes. Similarly, isomeric peptides can have distinct biological activities, and failing to distinguish them can lead to incomplete or misleading results.

The ZenoTOF 7600+ system leverages cutting-edge resolution and detection capabilities to address these challenges. By providing a clear and accurate view of these molecular details, the system enables researchers to understand disease mechanisms at a deeper level. This knowledge is invaluable for identifying drug targets, designing therapies, and even predicting how patients might respond to treatments. In essence, this precision helps bridge the gap between basic research and clinical application.

For researchers thinking about adopting advanced proteomics technologies, what should they consider when choosing a mass spectrometry system that aligns with their specific research goals?

When choosing a mass spectrometry system, researchers need to think about their specific goals and challenges. Are they focused on discovering low-abundance biomarkers, studying PTMs, or conducting high-throughput analyses? The ideal system should provide the sensitivity, speed, and flexibility to address these needs.

The ZenoTOF 7600+ system is designed to excel in all these areas. It offers unmatched sensitivity, lightning-fast scanning, and robust data quality, all within a user-friendly platform. Additionally, its ability to handle diverse applications—such as single cell proteomics, biomarker quantification, and disease mechanism studies—makes it a versatile choice for a wide range of research objectives.

How do you envision the future of this technology? Are there any upcoming trends or innovations in proteomics that you’re excited about?

The future of proteomics is incredibly exciting. I see single cell proteomics and spatial omics as the next big frontiers. These approaches will allow us to explore protein expression and modification with unprecedented resolution, unlocking insights into cellular heterogeneity and tissue-specific functions.

I’m also excited about the integration of artificial intelligence (AI) and machine learning in proteomics workflows. These technologies will revolutionize data analysis, making it faster, more accurate, and accessible to researchers with varying levels of expertise.

With innovations like the ZenoTOF 7600+ system, we’re laying the foundation for a future where proteomics isn’t just for specialists — it’s a tool that can be used broadly to answer fundamental questions in biology, accelerate drug discovery, and ultimately contribute to improving patient outcomes. The possibilities are limitless, and I’m thrilled to be part of this journey.

This interview has been condensed and edited for clarity.