‘Translating Proteomics’ explores the science of proteomics and its growing impact on biological research, biomarker discovery, drug development, food and energy security, and a range of other timely topics. Hosts Parag Mallick Ph.D. and Andreas Huhmer Ph.D. of Nautilus Biotechnology aim to share their perspectives on important issues in proteomics, deepen your love of science, and prompt you to question assumptions about what may be possible.
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Tau proteoform analysis – Key takeaways from our recent Nature Methods publication
Episode 29
Wednesday, September 16, 2026 • Duration 31:07
Translating Proteomics hosts Parag Mallick and Andreas Huhmer discuss our new Nature Methods paper, “Large-scale single-molecule analysis of tau proteoforms.” This publication describes how the Nautilus Voyager™ Platform can be used to quantify proteoforms derived from the neurodegeneration-associated tau protein. These proteoforms are defined by their unique combinations of post-translational modifications and isoform specific sequences. They may make powerful next-generation biomarkers or drug targets, but few technologies can measure them today.
In the episode, Parag and Andreas discuss:
What proteoforms are and why it’s critical to study them to understand biology.
How the Nautilus Voyager™ Platform quantifies proteoforms.
The key findings from the tau proteoform analyses in the paper.
Potential applications of these findings.
The Nautilus Voyager™ Platform as a powerful foundational technology.
Proteomics Hot Takes with Sheri Wilcox, Andreas Huhmer, and Parag Mallick
Episode 28
Wednesday, July 22, 2026 • Duration 48:03
On the latest episode of the Translating Proteomics podcast, Nautilus VP of Scientific Engagement and proteomics industry expert Sheri Wilcox joins hosts Parag Mallick and Andreas Huhmer for a thought-provoking discussion of their proteomics "hot takes.”
Each “hot take” is a provocative opinion on a topic in proteomics. Specifically, they cover:
Insufficient biological validation is one of the biggest problems in proteomics.
Antibody validation remains a distributed, inconsistent, lab-by-lab responsibility, and this model for validation may not be sustainable going forward.
AI cell models are overhyped.
Check out the episode for deep explorations of each of these hot takes and their potential remedies.
After listening, be sure to let us know whether you agree, disagree, or have your own hot take to share!
AI and Statistics in Proteomics and Systems Biology
Episode 27
Wednesday, February 25, 2026 • Duration 46:11
Professor Olga Vitek has a deep understanding of statistics, machine learning, and computational biology. She puts her know-how to work to develop computational tools enabling high-quality proteomic analysis and systems biology approaches. She hopes to apply these tools to the quantitative analysis of large-scale mass spectrometry-based investigations and thereby advance our understanding of organismal function. In this episode, Parag and Professor Vitek discuss:
Why statistics is important for experimental design
How statistics and AI can help researchers understand biology
Gaps keeping us from using AI and statistics to their maximum potential in biology
Ness et al., 2018 show how statistical methods can guide the selection of experiments that optimally enhance understanding
OMICS IN SPACE
Episode 26
Wednesday, February 4, 2026 • Duration 51:14
Host Parag Mallick chats with Professor Afshin Beheshti who is a Professor of Surgery, Director of the Center for Space Biomedicine, and Associate Director of the McGowan Institute for Regenerative Medicine at the University of Pittsburgh. In addition, Professor Beheshti has a visiting researcher appointment at the Broad Institute of MIT and Harvard and is president of two non-profits – the COVID-19 International Research Team and Kwaai. The latter aims to democratize access to artificial intelligence through the design, construction, and maintenance of a free personal AI called Kwaai.
Professor Beheshti’s research covers a range of topics focused on how circulating mirco RNAs and mitochondria impact health, but this conversation focuses primarily on Professor Beheshti’s work advancing our understanding of how spaceflight impacts biology. We cover:
How research on spaceflight and biology is done
Gaps that remain in our understanding of spaceflight and biology
Omics studies of spaceflight and biology
How studying spaceflight and biology enhances our understanding of human health more broadly
"Provides open access to biological and physical science datasets from spaceflight and ground studies, enabling data reuse for discovery and innovation."
Study on molecular biomarkers and frailty phenotypes in space
Overbey et al., 2024.
Reflections on Proteomics - 2025 Yea-End Wrap-Up
Episode 25
Monday, December 22, 2025 • Duration 35:51
On this episode of Translating Proteomics, Parag and Andreas share their reflections on proteomics developments in 2025 largely inspired by their observations at the World HUPO 2025 conference in Toronto. Whether you agree, disagree, or simply want to share some of your own observations on proteomics, please post your thoughts in the comments.
We look forward to even more exciting developments in 2026!
Chapters
00:00 - 00:35 – Intro
00:36 – 07:00 - Increased focus on applications of proteomics and less on method development
Learn more about One Health from our conversation with Professor Jennifer Geddes-McAlister
Hosts, Microbes, Molecular Pharming, and More with Professor Jennifer Geddes-McAlister
Episode 24
Thursday, November 6, 2025 • Duration 44:16
On this episode of Translating Proteomics, Parag speaks with Professor Jennifer Geddes-McAlister from the University of Guelph. Professor Geddes-McAlister is an expert at using proteomics to study host-microbe interactions from a systems biology perspective. Her exciting work spans studies of pathogenic fungi all the way to engineering plants to produce pharmaceutics (so-called “molecular pharming"). On top of all that, Professor Geddes-McAlister also founded “Moms in Proteomics” to support and encourage an intentional focus on the inherently unique physical, emotional, and biological commitments of Mothers, and the ensuing balance required to excel within the diverse STEM fields encompassing Mass-Spectrometry-based proteomics.
Dive into this episode to:
Learn why it’s critical to study hosts, pathogens, and molecular pharming from a systems point of view
Discover what Professor Geddes-McAlister is excited about for the upcoming Human Proteome Organization (HUPO) conference
Find out what “Moms in Proteomics” has planned for HUPO
Chapters
00:00 - Intro
01:39 - Professor Geddes-McAlister's initial interest in host-microbe interactions
06:13 - Why it's important to study host-microbe interactions
08:10 - Pathogens vs helpful microbes
10:06 - Thinking about microbes through the lens of "One Health"
14:34 - Why Professor Geddes-McAlister works primarily in proteomics as opposed to other omes
19:44 - Professor Geddes-McAlister's favorite thing that she's learned from the proteome and couldn't learn from the other omes
24:56 - Molecular pharming
29:35 - The need for accessibility in proteomics
- The need for all-in-one workflows in proteomics
Resources
“Ask me anything” with Parag Mallick, Andreas Huhmer, and featuring special guest Don Kirkpatrick, Ph.D.
Episode 23
Tuesday, July 15, 2025 • Duration 46:20
On this episode of Translating Proteomics, Parag, Andreas, and special guest Don Kirkpatrick answer questions submitted by the Translating Proteomics community. They cover:
Needs in plasma proteomics
How proteomics impacts drug development – with special guest Don Kirkpatrick, Ph.D.!
How lifestyle impacts the proteome
How the Nautilus Proteome Analysis Platform is impacting tau and Alzheimer’s disease research
References
Shome et al., 2022 - Serum autoantibodyome reveals that healthy individuals share common autoantibodies
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
Chapters:
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
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.
Proteomics Podcast Crossover - The Proteomics Show
Episode 20
Wednesday, April 2, 2025 • Duration 48:07
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
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Nonprofit "building a no-cost open source Personal AI assistant"
25:08 – 30:05 – Recognition of the need to assess quality across proteomics workflows
30:06 – 32:19 – Less of a focus on spatial proteomics this year than in past years
32:20 – 35: 13 - Parag and Andreas share their predictions for 2026
35:14 – End – Outro
34:09
36:08 - HUPO 2025
39:56 - Moms in Proteomics
42:36 - The future of proteomics
43:59 - Outro
Geddes et al., 2015. Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A
https://pubmed.ncbi.nlm.nih.gov/26453029/
Some of Professor Geddes-McAlister’s early work using proteomics to study pathogenic fungi
Prudhomme et al., 2024. Bacterial growth-mediated systems remodelling of Nicotiana benthamiana defines unique signatures of target protein production in molecular pharming
Researchers from Professor Geddes-McAlister’s lab use multiomic techniques to discover factors impacting the production of a pharmaceutical in an engineered plant
Woods et al., 2023. A One Health approach to overcoming fungal disease and antifungal resistance
Dr. Ginty wanted to acknowledge the many people she’s worked with on Cell DIVE and as part of HuBMAP. She stresses that these are highly collaborative projects, and just some of the many great team members she's worked with are listed below.
Cell DIVE:
Anup Sood, Sean Dinn, Yunxia Sui, Sanghee Cho, John Graf , Kathleen Bove, Musodiq Bello, Sudeshna Adak, Michael Lazare, Anirban Bhaduri, Thomas Treynor, Dileep Vangasseri, Alberto Santamaria-Pang, Maureen Bresnahan, Micheal Gerdes, Megan Rothman, Colin McCullough, Chris Sevinsky, Liz McDonough, Christine Surrette, Max Seel, Alex Corwin, Bob Filkins, Kevin Kenny, Brion Sarachan, Mike Montalto, Christoph Hergersberg, John Burczak, Jens Rittscher, Steve Zingelewicz, Dr. Sunil Badve (Emory U), Dr. Yesim Gokmen Polar (Emory U), Eli Lilly collaborators
HuBMAP:
Lou Falo (U. Pitt), Arivarasan Karunamurthy (U. Pitt), John Hickey (Duke), Chenchen Zhu (Stanford), Ioannis Vlachos (BIDMC), Liz McDonough (GE HealthCare Technology and Innovation Center [HTIC]), Sammi Abate (GE HealthCare Technology and Innovation Center [HTIC]), Soumya Ghose (GE HealthCare Technology and Innovation Center [HTIC]), Christine Surrette (GE HealthCare Technology and Innovation Center [HTIC]), Dr. Katy Borner (Indiana U)
