On this episode of Translating Proteomics, host Parag Mallick discusses Spatial Proteomics with special guest Fiona Ginty Ph.D. Fiona is a Senior Principal Scientist in Precision Diagnostics at the GE Healthcare Technology & Innovation Center. She is a leader in the development of spatial proteomics technologies and their application in precision diagnostics and medicine.

Their discussion covers:

· How Fiona began working in spatial proteomics

· Why spatial biology is important

· What the future holds for spatial biology

00:00 – Introduction

01:54 – Fiona’s journey to biology

05:26 – Fiona’s transition to tool development

07:20 – Working at GE Research

11:26 – Identifying the importance of spatial biology

14:43 – How Cell DIVETM works

18:25 – The importance of single cell

23:01 - When Fiona realized the technology worked

28:04 – Spatial biology projects Fiona is excited about

30:08 – Fiona’s role in HuBMAP

36:50 – Learnings from HuBMAP so far

38:35 – The future of spatial proteomics in the clinic

46:56 – Current limits on spatial proteomics

49:56 – Current and future uses of AI in spatial proteomics

53:30 – The most exciting thing Fiona learned in her spatial proteomics journey

56:08 – Outro

Method of the Year 2024: Spatial Proteomics

Paper covering the spatial proteomics technology Fiona worked on at GE Healthcare

• Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue

HubMAP – Human BioMolecular Atlas Program

Human Tumor Atlas Network

Cell DIVE Multiplex Imaging Solution

Papers discussing what makes colorectal cancer cells undergo apoptosis in response to chemotherapy

• An atlas of inter- and intra-tumor heterogeneity of apoptosis competency in colorectal cancer tissue at single-cell resolution
• Integrated multiplex analysis of cell death regulators in stage II colorectal cancer suggests patients with ‘persister’ cell profiles fail to benefit from adjuvant chemotherapy

Paper discussing how the distance between tumor cells and cytotoxic t-cells correlates to caspase level

• Spatial effects of infiltrating T cells on neighbouring cancer cells and prognosis in stage III CRC patients - Azimi - 2024 - The Journal of Pathology - Wiley Online Library

Paper showing it takes 3 hits from cytotoxic...

On this special episode of Translating Proteomics, Parag and Andreas break down the basics of proteomics — perfect for anyone with a background in molecular biology looking to get started in the field.

Seasoned experts: We hope you can share this episode as a teaching tool or to inspire others to explore proteomics.

Parag and Andreas cover the following questions in the episode, and links to additional Nautilus resources can be found below each question.

What is proteomics?

• Blog post – What is proteomics? Techniques, applications, and methods

What are key questions proteomics can answer?

• Blog category – Applications of proteomics

Why is it important to measure the proteome?

• FAQ on the Nautilus Resources page
• Blog post – Genomics vs. proteomics: Two complementary perspectives on life

What can and can't you do with proteomics?

• Translating Proteomics episode – Plasma Proteomics: The Dream and the Nightmare
• Learn how the Nautilus Platform is designed to enable comprehensive broadscale proteomics and targeted proteoform studies

What are key proteomics methods and techniques?

• Blog series – Traditional protein analysis methods
• Blog series – Next-generation proteomics technologies

What are the major pitfalls when doing proteomics?

What are the challenges in proteomic data analysis?

• Translating Proteomics episode – Biology in Space and Time
• Blog post – What is multiomics?

What are people excited about in proteomics?

• Translating Proteomics episode – Poised for a Proteomics Breakthrough
• Translating Proteomics episode - US HUPO 2025 – Key Takeaways, Trends, and Future Directions for Proteomics
• Translating Proteomics episode –

If you listened to our episode focused on science communication featuring proteomics leaders Ben Orsburn Ph.D. and Ben Neely Ph.D., then you've already heard about their excellent podcast, The Proteomics Show. On The Proteomics Show, they interview researchers in the proteomics community to learn about their motivations, their backstories, and their work. Today, we're sharing an episode of The Proteomics Show where the Bens interview Translating Proteomics host Parag Mallick. Check it out to learn about Parag's journey to proteomics, his efforts advocating for open data sharing, and his work as a professional magician.

After listening, be sure to check out more episodes of The Proteomics Show on their feed where you'll find over 70 interviews with many, many interesting people in the proteomics community. Find their feed here:

https://us-hupo.org/Podcasts

On this episode of Translating Proteomics, hosts Parag Mallick and Andreas Huhmer discuss their recent experience at the 2025 US Human Proteome Organization conference or US HUPO. Their conversation covers:

· The rising use of multiple proteomics platforms

· Advances in multiomics

And

· What they hope to see at the next US HUPO

Chapters:

00:00 – Introduction

01:47 – Things Parag and Andreas were most excited about going into US HUPO

06:19 - Trends Parag observed at US HUPO

· A bifurcation between studies that focused on measuring many proteins and those that focused on a specific biological process

· People increasingly using multiomics to wholistically understanding biology as opposed to a means of comparing the different omes

· A shift to researchers using multiple proteomics platforms

11:44 – The rising prominence of proteoforms at US HUPO

15:50 – The future of proteomics as informed by US HUPO

18:06 – What Parag and Andreas hope to see at the next US HUPO

19:57 - Outro

On this episode of Translating Proteomics, host Parag Mallick speaks with special guests doctors Ben Neely and Ben Orsburn, leaders in the proteomics community and hosts of “The Proteomics Show” podcast. Their insightful conversation focuses on the role of communication in proteomics and covers:

· Impactful things they’ve learned while hosting The Proteomics Show

· How their communication efforts have changed their research

· Barriers to proteomics becoming more popular in the life sciences and in the broader public

00:00 – 03:04 – Intro

03:04 – 07:23 – Why the Bens created "The Proteomics Show"

07:23 – 10:42 – Ways the proteomics show has impacted the Bens’ research

10:42 – 16:44 – Every scientist is interesting!

16:44 – 20:36 – Ways the Bens' communication efforts have changed their research

20:36 – 25:08 – Trends in proteomics

25:08 – 35:34 – Barriers to communication between the proteomics community and others in the life science

34:34-48:34 - Barriers to communication between the proteomics community and the broader public

48:34 - End - Outro

• The Proteomics Show - Ben Neely and Ben Orsburn host this podcast sponsored by the Human Proteomics Organization. On it, they interview proteomics researchers in a “fireside chat” format. Their conversations cover not just the latest research, but also their guests’ motivations, hobbies, and histories. Definitely check it out!
• News in Proteomics Research - Ben Orsburn's blog on the latest developments in proteomics.
• Proteomics, the next truly massive investment opportunity - Forbes article on the potential of proteomics.
• The Magic School Bus Rides Again - Recently rebooted version of The Magic School Bus. Will we see an episode featuring proteomics?

On this episode of Translating Proteomics, hosts Parag Mallick and Andreas Huhmer discuss the many ways proteomics can impact our interactions with food. Some of the topics they touch upon in this wide-ranging conversation include:

· Proteomics and food quality

· Proteomics and food safety

· Developing new kinds of food with proteomics

00:00 – 01:23 – Introduction

01:23 – 03:27 – Proteomics and alcohol fermentation

03:27 – 05:24 – Food properties and their relationship with molecular composition

05:24 – 07: 42 – How can we use proteoforms to improve food quality?

07:42 – 11:49 – Proteomics to aid plant and animal breeding

11:49 – 14:35 – Proteomics, Food Safety, and Food Security

14:35 – 17:05 – Proteomics and food authenticity

17:05 – 20:36 – Proteomics and terroir

20:36 – 22:48 – Proteomics, the microbiome, and health

22:48 – 24:29 – A fun party trick

24:29 – 30:24 – Creating new foods and flavors

30:24 – 34:33 – Designing food for space

34:33 – End – Outro

The post-translational modification landscape of commercial beers (Kerr et al. 2021)

· Paper looking at the ways post-translational modification differ between different beers and how protein content relates to the properties of foam

Heat shock and structural proteins associated with meat tenderness in Nellore beef cattle, a Bos indicus breed (Carvalho et al. 2024)

· Paper looking at the relationship between proteins and meat tenderness

Comprehensive proteome analysis of bread dicphering the allergenic potential of bread wheat, spelt and rye (Zimmermann et al. 2021)

· Research measuring the levels of allergens in different kinds of bread

Differential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to non-optimal temperatures under anaerobic conditions

· Study using proteomics to reveal how yeast adapt to growth at different temperatures

On this episode of Translating Proteomics, co-hosts Parag Mallick and Andreas Huhmer of Nautilus Biotechnology discuss the reproducibility crisis in biology and specifically focus on how we can enhance reproducibility in computational proteomics. Key topics they cover include:

• What the reproducibility crisis is

• Factors that make it difficult to replicate multiomics research

• Steps we can take to make biology research more reproducible

Chapters

00:00 – 01:20 – Introduction

01:20– 03:10 – What is reproducibility in research and why is it important?

03:10 – 05:42 – Recent work from the Mallick Lab focused on computational proteomics reproducibility

05:42 – 09:32 – Ways to help improve reproducibility in computational proteomics – More detailed documentation, moving beyond papers as our main form of documentation, and ensuring computational workflows are available,

09:32 – 11:30 – Why Parag got interested reproducibility – Attempts to build AI layers on top of current workflows

11:30 – 14:00 – The need to create repositories of analytical workflows codified in a structured way that AI can learn from

14:00 – 15:24 – A role for dedicated data curators

15:24 – 18:31 – Moving beyond the idea of study endpoints and recognizing data as part of a larger whole

18:31 – 21:32 – How does AI fit into the continuous analysis and incorporation of new datasets

21:32 – 23:36 – The role of AI in helping researchers design experiments

23:36 – 27:25 – Three things we can do today to increase the reproducibility of computational proteomics experiments:

· Be clear about the stated hypothesis

· Document analyses through workflow engines and containerized workflows

· Advocate for support for funding for reproducibility and reproducibility tools

27:25 – End – Outro

Resources

Parag’s Gilbert S. Omenn Computational Proteomics Award Lecture

o In this lecture, Parag describes his vision for a more reproducible future in proteomics

Nature Special on “Challenges in irreproducible research”

o A list of articles and perspective pieces discussing the “reproducibility crisis” in research

Why Most Published Research Findings Are False (Ioannidis 2005)

o Article outlining many of the issues that make it difficult to reproduce research findings

Reproducibility Project: Cancer Biology

o eLife initiative investigating reproducibility in preclinical cancer research

Center for Open Science Preregistration Initiative

o Resources for preregistering a hypothesis as part of a study

National Institute of Standards and Technology (NIST)

o US government agency that aims to...

On this episode of Translating Proteomics, co-hosts Parag Mallick and Andreas Huhmer of Nautilus Biotechnology discuss how clinical researchers can leverage proteomics for drug development. Some of the themes covered in this episode include:

· Proteomics and pre-clinical models

· How proteomics can drive patient selection

· Choosing the right end points in clinical trials

Chapters

00:00 – 01:06 – Introduction

01:06 – 06:51 – Proteomics in pre-clinical studies

06:51 – 11:40 – The importance of choosing the right model for preclinical work

11:40 – 17:10 – How proteomics is used in Phase I/II clinical trials

17:10 – 19:29 – Proteomics tools in patient selection

19:29 – 24:33 – Useful information that we get from proteomics that we can’t get from genomics or transcriptomics

24:33 – 28:14 – Proteomics in Phase III clinical trials and picking the best indications of drug efficacy

28:14 – 29:19 - Understanding why clinical trials fail

29:19 – End - Outro

Resources

• The National Cancer Institute’s webpage covering how clinical trials work
• Preprint on the miBrain model - An example of a new in vitro brain model
• Geary et al., 2021 - Discovery and Evaluation of Protein Biomarkers as a Signature of Wellness in Late-Stage Cancer Patients in Early Phase Clinical Trials
• Wasko et al., 2024 - Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer
• The NCI-MATCH trail: Lessons for precision oncology – Report on a large-scale trial using genomic biomarkers to match cancer patients to treatments
• Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer – Study using proteomics to understand mechanisms of resistance to a cancer drug