Translating Proteomics

Nautilus Biotechnology
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‘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.

  1. OMICS IN SPACE

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    OMICS IN SPACE

    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 doneGaps that remain in our understanding of spaceflight and biologyOmics studies of spaceflight and biologyHow studying spaceflight and biology enhances our understanding of human health more broadly ResourcesTrivedi Institute for Space and Global Biomedicine New Institute at the University of Pittsburgh focused on “advancing human health through space-driven innovation” NASA Open Science Data Repository "Provides open access to biological and physical science datasets from spaceflight and ground studies, enabling data reuse for discovery and innovation." Camera et al., 2024. Agining and putative frailty biomarkers are altered by spaceflight Study on molecular biomarkers and frailty phenotypes in space Overbey et al., 2024. The Space Omics and Medical Atlas (SOMA) and international astronaut biobank An “integrated data and sample repository for clinical, cellular, and multi-omic research profiles” from a variety of space missionsSpace Omics and Medical Atlas (SOMA) website Corti et al., 2024. To boldly go where no microRNAs have gone before: spaceflight impact on risk for small-for-gestational-age infants Explores how miRNA signatures of “small-for-gestational-age” are impacted by the space environment Beheshti et al., 2013. Age and space irradiation modulate tumor progression: implications for carcinogenesis risk Some of Professor Beheshti’s early...

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  2. Reflections on Proteomics - 2025 Yea-End Wrap-Up

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    Reflections on Proteomics - 2025 Yea-End Wrap-Up

    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! Chapters00:00 - 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 https://youtu.be/JFwvTdkb5bw 07:01 – 12:47 - Increase in people talking about the importance of proteoforms Learn more about proteoforms in our episode featuring proteoform pioneer Professor Neil Kelleher https://youtu.be/3pPuxVrMxpw 12:47 – 17:26 - An increase in multiomics studies 17:27 – 20:03 - A shift to larger scale proteomics studies For a great example of a multi-platform comparison study, check out Kirsher et al., 2025 https://www.nature.com/articles/s42004-025-01665-1 20:03 – 25:07 - Increased integration of AI into proteomics workflows For an example of how proteomics workflows can be modified with multiomic data, check out Suhre et al., 2025 https://www.nature.com/articles/s41588-025-02413-w 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

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  3. Hosts, Microbes, Molecular Pharming, and More with Professor Jennifer Geddes-McAlister

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    Hosts, Microbes, Molecular Pharming, and More with Professor Jennifer Geddes-McAlister

    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 viewDiscover what Professor Geddes-McAlister is excited about for the upcoming Human Proteome Organization (HUPO) conferenceFind out what “Moms in Proteomics” has planned for HUPO Chapters00:00 - 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 34:09 - The need for all-in-one workflows in proteomics 36:08 - HUPO 2025 39:56 - Moms in Proteomics 42:36 - The future of proteomics 43:59 - Outro ResourcesGeddes 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 https://onlinelibrary.wiley.com/doi/10.1111/pbi.14342 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 https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wsbm.1610 Review on the importance of incorporating “One Health” principals into efforts to fight pathogenic fungi Moms in Proteomics website https://momsinproteomics.ca Learn all about the Moms in Proteomics initiative and its international community

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  4. “Ask me anything” with Parag Mallick, Andreas Huhmer, and featuring special guest Don Kirkpatrick, Ph.D.

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    “Ask me anything” with Parag Mallick, Andreas Huhmer, and featuring special guest Don Kirkpatrick, Ph.D.

    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 proteomicsHow proteomics impacts drug development – with special guest Don Kirkpatrick, Ph.D.!How lifestyle impacts the proteomeHow the Nautilus Proteome Analysis Platform is impacting tau and Alzheimer’s disease research ReferencesShome et al., 2022 - Serum autoantibodyome reveals that healthy individuals share common autoantibodies https://www.sciencedirect.com/science/article/pii/S2211124722006489 LaBaer Lab paper investigating autoantibody levels in plasma and their relationship to health. Sylman et al., 2018 - A Temporal Examination of Platelet Counts as a Predictor of Prognosis in Lung, Prostate, and Colon Cancer Patients https://www.nature.com/articles/s41598-018-25019-1 Mallick lab paper investigating temporal changes in platelets and their associations with cancer biology. Krönke et al., 2014 - Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells https://www.science.org/doi/10.1126/science.1244851 Seminal paper describing selective protein degradation caused by lenalidomide. Fink and Ebert 2015 - The novel mechanism of lenalidomide activity https://ashpublications.org/blood/article/126/21/2366/34644/The-novel-mechanism-of-lenalidomide-activity Review of research elucidating the mechanisms of lenalidomide activity Ndoja et al., 2025 - COP1 Deficiency in BRAFV600E Melanomas Confers Resistance to Inhibitors of the MAPK Pathway https://www.mdpi.com/2073-4409/14/13/975 Describe links between kinase inhibitor vemurafenib and changes in ETV transcription factor degradation Song et al., 2022 - RTK-Dependent Inducible Degradation of Mutant PI3Kα Drives GDC-0077 (Inavolisib) Efficacy https://aacrjournals.org/cancerdiscovery/article/12/1/204/675622/RTK-Dependent-Inducible-Degradation-of-Mutant-PI3K Use proteomics to discover that inavolisib acts through selective degradation of mutant PI3Kα Canon et al., 2019 - The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity https://www.nature.com/articles/s41586-019-1694-1 Covers the development of an inhibitor of KRAS mutant KRAS (G12C). Schneider et al., 2024 - Feeding gut microbes to nourish the brain: unravelling the diet-microbiota-gut-brain axis https://www.nature.com/articles/s42255-024-01108-6 Review on the gut-brain axis Webpage for Johanna Lampe’s Lab at Fred Hutch Cancer Center a href="https://www.fredhutch.org/en/faculty-lab-directory/lampe-johanna.html" rel="noopener noreferrer"...

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  5. Spatial Proteomics with Fiona Ginty Ph.D.

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    Spatial Proteomics with Fiona Ginty Ph.D.

    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 56:08 – Outro Resources: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 resolutionIntegrated 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...

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  6. Intro to Proteomics

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    Intro to Proteomics

    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 pageBlog 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 NightmareLearn 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 methodsBlog 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 TimeBlog post – What is multiomics? What are people excited about in proteomics? Translating Proteomics episode – Poised for a Proteomics BreakthroughTranslating Proteomics episode - US HUPO 2025 – Key Takeaways, Trends, and Future Directions for ProteomicsTranslating Proteomics episode – a href="https://www.nautilus.bio/blog/translating-proteomics-episode-10-protein-function-201-with-kathryn-lilley/" rel="noopener noreferrer"...

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  7. Proteomics Podcast Crossover - The Proteomics Show

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    Proteomics Podcast Crossover - The Proteomics Show

    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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  8. US HUPO 2025 - Key Takeaways, Trends, and Future Directions for Proteomics

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    US HUPO 2025 - Key Takeaways, Trends, and Future Directions for Proteomics

    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

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‘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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    Translating Proteomics