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Tanveer Batth @tsbatth.bsky.social · 10/02/2026

Me every single time i need to prepare a LCMS setup to run a couple of samples ... #proteomics

Tanveer Batth @tsbatth.bsky.social · 25/03/2025

As pointed out by someone else on LinkedIn, the new anti obesity peptide recently published in Nature has the following MS/MS spectra 🤔🫣 Paper for reference: www.nature.com/articles/s41... #proteomics #TeamMassSpec

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Tanveer Batth @tsbatth.bsky.social · 05/01/2025

After being asked to try 5% FDR to identify a protein. #proteomics and #teammassspec things

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Tanveer Batth @tsbatth.bsky.social · 01/01/2025

TIL about "lasso peptides." #Peptides that make a literal lasso where the C-terminal chain loops through the ring. Learn more here: is.gd/R1Vr8a #science #proteins How would they separate on reversed-phase material and ionize/fragment in a MS ? 🤔

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Tanveer Batth @tsbatth.bsky.social · 03/12/2024

Great slide by Ruedi Aeberold who kicks of #DAPSOC as the first speaker. #proteomics has been constantly outperforming "Moore's law" in regards to sensitivity (amount required) and throughput #science

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Tanveer Batth @tsbatth.bsky.social · 16/11/2024

Me on here 👏🏽👍🏽🔥🎉

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

But no method is perfect, including this one. Each has its disadvantages and advantages and I think it important to be aware of the limitations. For example we thought we found a new Metformin target, but it is most likely an artifact of the method.

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

We validated a low affinity target (protein called Pirin) for Ibuprofen, which was found in different extracts.

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

This visualization is also a very nice way to look at shared drug targets from our dataset. A nice way to look at some complex data. Btw, the Cytoscape networks for all the drugs are downloadable (details below)

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

More details in the paper of course, but Nadya (co-author) used the resulting data to beautifully visualize drug-protein targets, I think it looks really cool.

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

Briefly, the strategy involves using the entire dataset to control for each compound (within each organ/cell extract experiment) to exclude drugs that are structurally similar or have known shared targets. We used the database drugcentral.org and the Tanimoto index for this.

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

I tried to take this up one more level and see if this technique could work on rat organs ex-vivo. Once the organs were collected, I tried to gently extract soluble proteins and use the same benchmark on different extracts. It works well for most extracts.

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

We used an optimized version of the PISA approach where we forgo the use of TMT reagents, use a label-free DIA MS method, optimize heating temperatures + filter plates. It works well in our Staurosporine ("positive control") benchmark. Look at this beautiful volcano plot 🌋

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

TPP can measure melting point of 1000's of proteins from a complex mixture (ie. cells, organ extracts), which can change if a protein is targeted by a drug. There are variations of this principal that integrate melting curve such as proteome integral solubility alteration (PISA)

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

Our totally unbiased view is: if you are trying to determine protein targets, start with measuring the actual proteins (ie. mass spectrometry [MS] based proteomics). One the most prominent method to this is based on Thermal Proteome Profiling (or its many variations such as PISA)

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

And there are MANY methods that attempt find these unknown targets, ultimately it will be a trade off between speed, specificity, and the proteome depth. There is NO perfect method, and each will have its advantages and disadvantages.

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Tanveer Batth @tsbatth.bsky.social · 10/11/2024

Ok, going to try to repost the thread on here as well :) --------- I'm happy to report the publication of our latest #proteomics paper has been published in Nature Communications . Thanks to the reviewers and editors who helped us improve the manuscript! rdcu.be/dZLbk A small 🧵below

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