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Chris Whelan

@chrisdwhelan.bsky.social
365 followers 236 following 31 posts

Very infrequent Bluesky poster. Interested in population proteomics, genetics, neuroscience & biomarker development. 🇮🇪🧠🧬

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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
*Correction* - the tool mentioned here (4) is "Help Me Choose", not Help Me Combine.
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
No worries at all! Affinity methods are getting most of the attention from orthogonal disciplines (I am partly responsible for this) and I'm hoping this tool directs the right people towards mass spec vendors - these will largely be non-MS scientists as you say.
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
Thanks for correcting! We found it difficult to evaluate the mass spec platforms themselves (e.g., Astral, timsTOF) but the services run on top of those platforms like Biognosys and Seer are well-documented and were easier to include.
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
9. APT is of course completely free and its code is available at DOI: 10.5281/zenodo.22697192 We expect people will disagree with some of the scores, but at the very least, we hope the search + browse features on the Protein Coverage tab will save folks some time!
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
Vendors often push their versions of the truth in their marketing. APT tries to cut through that noise. However, there are so many talented and hardworking scientists at each company who are genuinely passionate about building the best products. For them, online tools are poor substitutes.
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
...After this, they come back with more nuanced follow-up questions, and following a more involved conversation, I usually point them towards the vendors and towards other proteomics researchers for a second, third, fourth, ...nth opinion.
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
8. And - perhaps most importantly - it's not supposed to replace conversations with the people who work at these companies or the experts in each space. I've pointed people at APT when they approach me for my proteomics opinions. It saves us both a headache discussing the basics...
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
7. This was a fun project that I built to help *myself* navigate the increasingly complex technology landscape. It evolved into a full-blown website and pre-print once my co-author (Karl) and I realized that it could benefit the broader field, too. It needs peer review, and its scores will change.
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
...Therefore, our second tool, "Help Me Combine", helps determine when it makes sense to combine, e.g., Seer nanoparticle enriched mass spec with Olink, or bottom-up MS with Alamar NULISA, or Nomic with SomaLogic, etc.: aptatlas.org#combine
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
6. More & more often, I have found myself recommending multiple platforms over a single winner-takes-all approach. Despite mostly publishing w/ affinity platforms, I strongly believe MS should be combined with affinity tech in many scenarios...
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
5. We'll add more platforms once enough peer-reviewed evidence accumulates and, ideally, once we have a chance to deploy those platforms directly. We keep track of emerging platforms here: aptatlas.org#platforms
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
...its accompanying recommendations. We pressure-tested those recommendations across more than a million scenarios to make sure the recommendations are giving the six platforms an equal shake. Our conclusion was that it's fair... but we of course welcome feedback. aptatlas.org#chooser
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
4. We used these scores to power a tool called, "Help Me Combine". Proteomics power-users almost certainly don't need this, but genomics scientists, population health researchers, and newcomers to the field should *hopefully* benefit from its guided walk-through of study design and...
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
3. The scores are not absolute, and we fully expect them to change as new evidence emerges and as the manuscript goes through peer-review. They reflect good-faith interpretations of the published literature, combined with our own experiences, where relevant, in deploying each platform.
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
...(ix) how many samples they can process and how quickly [throughput], and (x) how much peer-reviewed evidence actually supports their scores.
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
...(iv) how well they detect low-abundance proteins [sensitivity], (v) their typical cost range per sample, (vi) whether they natively offer absolute quantitation, (vii) how well-validated they are across sample matrices, (viii) whether they detect pQTLs with minimal epitope effects...
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
...to score the six platforms on (i) how much of the 'canonical' proteome they captured [coverage], (ii) how reproducible their measurements are over time - i.e., low CVs [precision], (iii) how confidently their signals reflect their intended protein(s) [specificity]...
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
2. From there, it made sense to describe the platforms included in that catalog. Those descriptions naturally led to, "consider mass spec for X, consider affinity proteomics for Y". So, we gathered as much peer-reviewed evidence as we could, and combined it with our own judgements...
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
Some disclaimers: 1. This started because I found the process of determining which platform(s) capture which protein(s) on-the-fly extremely inefficient, so I built this searchable catalog to make it easier: aptatlas.org#proteins
aptatlas.org
Atlas of Proteomic Technologies (APT)
Compare commercial high-plex proteomics platforms by coverage, sensitivity, quantification, and cost, with evidence-based guidance on which platform, or pair of platforms, to run.
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Chris Whelan @chrisdwhelan.bsky.social · 16/09/2026
Today we announced the Atlas of Proteomic Technologies (APT), available at aptatlas.org. APT compares six proteomics technologies (Alamar, Biognosys, Nomic, Olink, Seer, Somalogic) across ten dimensions. We describe the resource in this pre-print: biorxiv.org/content/10.64898/2026.09.10.750723v1
biorxiv.org
Atlas of Proteomic Technologies: an evidence-based framework for selecting and combining commercial proteomics platforms
High-throughput proteomics now spans several technologies that differ in biological breadth, precision, specificity, sensitivity, cost, and method(s) of quantification; however, investigators currentl...
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Chris Whelan @chrisdwhelan.bsky.social · 11/01/2025
The UKB-PPP consortium should receive the first tranche of ~100k samples this autumn and subsequent tranches throughout 2026. Data releases to all approved UKB researchers will begin next year.
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Chris Whelan @chrisdwhelan.bsky.social · 10/01/2025
*Alden Scientific, Amgen/deCODE genetics, AstraZeneca, Bristol Myers Squibb, Calico Life Sciences, Genentech, GSK, Isomorphic Labs, Johnson & Johnson, Merck Group, Novo Nordisk, Pfizer, Regeneron and Takeda.
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Chris Whelan @chrisdwhelan.bsky.social · 10/01/2025
I'm deeply grateful to the hundreds of collaborators working across fourteen biopharmaceutical companies*, two technology vendors, and one remarkable biobank for making this possible.
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Chris Whelan @chrisdwhelan.bsky.social · 10/01/2025
This initiative again underpins the transformative value of public-private partnerships for drug development and healthcare and reemphasizes the quiet 'revolution' happening in the field of proteomics.
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Chris Whelan @chrisdwhelan.bsky.social · 10/01/2025
This will allow us to build foundational AI models for biological discovery, study biomarkers that change over time in response to changes in health states, identify surrogate blood biomarkers for MRI endpoints, and - ultimately - develop better medicines & diagnostics.
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Chris Whelan @chrisdwhelan.bsky.social · 10/01/2025
We will begin by profiling 300k samples, comprising approximately 250k samples collected at baseline visits and 50k samples taken at various follow-up assessments. We aim to incorporate an additional 250k baseline samples and 50k repeat samples pending additional funding.
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Chris Whelan @chrisdwhelan.bsky.social · 10/01/2025
I'm delighted to announce that the Pharma Proteomics Project will commence full-scale proteomic profiling of the UK Biobank in 2025. We have selected the Olink Proteomics Explore HT platform and Ultima Genomics UG 100 sequencers for this unprecedented study. www.ukbiobank.ac.uk/learn-more-a...
ukbiobank.ac.uk
Launch of world’s most significant protein study set to usher in new understanding for medicine
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Reposted by Chris Whelan
Veera Rajagopal @doctorveera.bsky.social · 12/12/2024
Association of polygenic scores for neuropsychiatric traits with self-reported professions based on analysis of 420k individuals from UK Biobank and Million Veteran Program. Look at the 'arts & design' category. Artistic talent comes at a cost--a piece of your mind :)
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Reposted by Chris Whelan
Eric Topol @erictopol.bsky.social · 11/12/2024
Could be combined in the future with a continuous sensor (implant) for real-time detection of proteins driving inflammation in high-risk individuals www.science.org/doi/10.1126/... @science.org
science.org
Active-reset protein sensors enable continuous in vivo monitoring of inflammation
Continuous measurement of proteins in vivo is important for real-time disease management and prevention. Implantable sensors for monitoring small molecules such as glucose have been available for more...
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Chris Whelan @chrisdwhelan.bsky.social · 21/11/2024
Possibly, but Alamar is low-plex by design (n~250) & captures many low-abundance proteins - not necessarily the most widely studied. Mike’s comment & Jochen’s review offer important perspectives; abundance levels seem to influence confidence in cross-platform detection (higher = more confidence).
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Reposted by Chris Whelan
Jochen Schwenk @jochwenk.bsky.social · 21/11/2024
Here we tried to provide some objective views to the reoccurring discussion: pubs.acs.org/doi/10.1021/... The key is to understand the biases and factors causing the differences in the data. Those can include and do go beyond the antibodies.
pubs.acs.org
The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends
Recent improvements in proteomics technologies have fundamentally altered our capacities to characterize human biology. There is an ever-growing interest in using these novel methods for studying the ...
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Chris Whelan @chrisdwhelan.bsky.social · 21/11/2024
Yes, “good” is relative to what’s been reported before. It’s the median correlation across 217 commonly measured proteins, with a wide range overall. More documentation of the antibodies used +/ epitopes bound could partially address the problem, but might be impractical to implement.
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Chris Whelan @chrisdwhelan.bsky.social · 20/11/2024
We’ve found Olink & Alamar to correlate quite well (~60%) overall. Maybe unsurprising, since both are antibody-based. Lack of correlation b/w SomaScan & others might reveal interesting facets of the aptamer tech (protein folding, PTMs, etc) but 100% agree that infighting is bad for the field.
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Chris Whelan @chrisdwhelan.bsky.social · 20/11/2024
Loved participating in the ‘Advancing Multi-Omics to the Clinic’ meeting in beautiful Sydney this week. Fascinating talks from several KOLs (see photos for Ruedi Aebersold’s revised Central Dogma of Biology) & lots of encouraging interplay between mass spectrometry and affinity-based proteomics.
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