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Bini Ramachandran

@itsbinir.bsky.social
795 followers 342 following 731 posts

Mass Spectrometry/Proteomics nerd....

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Bini Ramachandran @itsbinir.bsky.social · 26/09/2026
Thanks.. I have been considering trimming.. Excluding that overexpressed protein from normalisation will give a better look at the scenario?? The challenge is that some of the proteins are exclusive in the sample where there is no overexpression of this protein..
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Bini Ramachandran @itsbinir.bsky.social · 26/09/2026
The overexpressed protein contributes to 20% of total protein abundance in samples.. global normalisation by summed or median abundance approach can bring technical bias due to this..
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Bini Ramachandran @itsbinir.bsky.social · 26/09/2026
Thanks very much.. I will check this out..
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Bini Ramachandran @itsbinir.bsky.social · 25/09/2026
A mundane question from a Friday evening brain.. If I have a protein overexpressing 20% more in a sample and it is the most abundant protein in that sample, how should I normalize the data for fold analysis for the rest of the proteins if an equal representative sample was analyzed.. #TeamMassSpec
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ypic.bsky.social @ypic.bsky.social · 22/09/2026
🔬 Ready to turn your proteomics idea into reality? The Student Proteomics Fund (SPF) is a student-focused grant designed to support students in bringing their proteomics experiments to life! 📅 Call opens: October 1st, 2026 ⏰ Submission deadline: November 30th, 2026
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Bini Ramachandran @itsbinir.bsky.social · 08/09/2026
I have been doing this for the past 5 years or so.. At times I sit and worry what if the brand stops manufacturing this model in the future and should I buy in bulk now and stock.. 🤔🤔
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Bini Ramachandran @itsbinir.bsky.social · 20/08/2026
The only place where it can be eliminated is in data completeness.. It is not detected in all samples tested.. But neither the other peptide hits..(2/2)
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Bini Ramachandran @itsbinir.bsky.social · 20/08/2026
How to validate these kinds of hits? These pass XCorr, Search engine score, deltaM, isolation interference and 1% FDR thresholds. All looks at visual inspection of spectra as well. (1/2)
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Bini Ramachandran @itsbinir.bsky.social · 20/08/2026
Thanks.. Good to know.. There is also a poly Proline hit.. That's common too??
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Bini Ramachandran @itsbinir.bsky.social · 20/08/2026
That's a frigging peptide spectrum match.. Playing with endogenous peptides on mass spec is funny.. 😊😊
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Bini Ramachandran @itsbinir.bsky.social · 18/08/2026
Hello #Astral users, Have you ever come across the ion foil adjustment failure error?? We have started seeing it since the tune was upgraded to 2.2 recently during the PM. The error interferes with the system getting ready to run a sample in the step where astral mass accuracy is checked with ICS.
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IonOpticks @ionopticks.com · 11/08/2026
One of the most overlooked factors in maintaining consistent, high-quality spray in nano-scale liquid chromatography is something you handle every time you connect your column: your capillary fitting. Thankfully, a little care & a few simple habits go a long way. Here's what to know: bit.ly/4zbjHd4
bit.ly
Caring for your capillary fitting: small habits for stable spray
One of the most overlooked factors in maintaining consistent, high-quality spray in nano-scale liquid chromatography is something you handle every time you connect your column: your capillary fitting ...
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Bini Ramachandran @itsbinir.bsky.social · 10/08/2026
On a similar note, I got a request last Friday evening to submit a bid proposal for a large cohort sample project by today..
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Bini Ramachandran @itsbinir.bsky.social · 07/08/2026
That's cool.. You have got superb clean samples.. Totally agree with the peptidomics comment.. We had to change the whole injection valve recently after a botched peptidomics project..
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Bini Ramachandran @itsbinir.bsky.social · 06/08/2026
For the nano columns, getting a 1000 injection would be a dream come true scenario..
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Bini Ramachandran @itsbinir.bsky.social · 29/07/2026
Thank you so very much for keeping us informed on the hot and happening in proteomics.. It would be a great loss for the mass spec proteomics community not having those updates.. All the very best with the new pastures with immunodiagnostics.. 🫡🫡
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Bini Ramachandran @itsbinir.bsky.social · 29/07/2026
Thanks.. haven't tried it.. don't have an Evosep.. Seems to work well for low input samples.. especially with automation options..
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Bini Ramachandran @itsbinir.bsky.social · 29/07/2026
This seems nice.. that's for sharing.. have to dig in..
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Bini Ramachandran @itsbinir.bsky.social · 28/07/2026
May I check how do you deal with the incomplete gut microbiome databases? Many are not fully sequenced and those have got many redundant entries in TrEMBL. Not to mention the challenges from homologous proteins from different species.. I am in the boat analysing the poop sample metaproteome now..
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Bini Ramachandran @itsbinir.bsky.social · 23/07/2026
SP3 with 1-5ug.. That sounds nice.. Manual or automated?? What is SPEC btw..
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Bini Ramachandran @itsbinir.bsky.social · 22/07/2026
S-traps were being considered for dirty detergent containing low input samples... These are at the max a couple of micrograms in total.. SP3 is the way to go for bulk proteomics.. SP3 for low input has been tricky though..
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Bini Ramachandran @itsbinir.bsky.social · 22/07/2026
In the world of astral and TimsTofs scale up is needed in terms of the number of samples that can be processed in parallel.. In gel digestion won't work when 100s samples need to be processed..
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Bini Ramachandran @itsbinir.bsky.social · 22/07/2026
In gel workflows do not scale up.
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Bini Ramachandran @itsbinir.bsky.social · 21/07/2026
A question to mass spectrometrists in the core facilities around the UK and Europe.. How are you finding the cost of S-traps for proteomics applications?? It looks like incorporation of S-traps in the workflow adds an additional £8 per sample.. It feels extraordinarily expensive..
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Sonja Blasche @sonjablasche.bsky.social · 16/07/2026
Our article "Common xenobiotics modulate gut microbial responses to low‑calorie sweeteners in vitro" is out! link.springer.com/article/10.1... With @kiranrpatil.bsky.social, @indraroux.bsky.social, @rbradley.bsky.social, @skamrad.bsky.social, @simonemozzachiodi.bsky.social, @itsbinir.bsky.social.
link.springer.com
Common xenobiotics modulate gut microbial responses to low‑calorie sweeteners in vitro - Molecular Systems Biology
The gut microbiota is implicated in adverse effects associated with low-calorie sweeteners. Yet, the direct impact of sweeteners on gut bacteria remains largely uncharacterized. Here, we report intera...
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ASMS @asms.org · 25/06/2026
Hey, #TeamMassSpec! Interested in a career in academia? #ASMS will host 2 free Zoom panel discussions ft. college faculty sharing insights on preparing your academic job application package and what to expect during the interview process. Register now! bit.ly/4c1VrR5
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Bini Ramachandran @itsbinir.bsky.social · 23/06/2026
Why waste biological memory to remember netflix password.. Save it in the password manager and it automatically logs you in.. 😉😉
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Bini Ramachandran @itsbinir.bsky.social · 23/06/2026
Never been a fan of the so-called number game.. However, it is indeed exciting when you get to see 100 precursors identified per second from biological samples, not just from a std digest.. Pretty stoked by having a front raw seat to witness the technology evolution through ages..😊😊 #MassSpecMusings
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Bini Ramachandran @itsbinir.bsky.social · 23/06/2026
21.0
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EMBL @embl.org · 22/06/2026
The EMBL #ARISE2 Fellowship Programme, funded by MSCA, opens for applications 30 June. This unique opportunity trains researchers to lead #ResearchInfrastructures & innovate in #LifeSciences. 🧪 🗓️ Join our webinar on Thursday, 2 July at 09:30 CET: embl-org.zoom.us/webinar/regi... #careers
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Bini Ramachandran @itsbinir.bsky.social · 22/06/2026
Yeah.. Project specific libraries seem to be the way to deal with +1 peptides.. I am doing the same for a non-tryptic peptide sample set as well.. I have to look more into the hybrid library options.. Thanks..
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Bini Ramachandran @itsbinir.bsky.social · 21/06/2026
Thanks for sharing this. Faced a similar issue in detecting +1 semi tryptic peptides on Spectronaut as well in library-free mode. The database used was a bit messy here. It wasn't a sequenced organism and had quite a few redundant and partial sequences. Curious to know how you resolved the issue.
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Bini Ramachandran @itsbinir.bsky.social · 20/06/2026
#TeamMassSpec, may I please check if there is a lab where Thermo #Ardia is seamlessly connected to multiple mass specs and process proteomics data processing and management on the server itself?? If yes, can I please have a brief chat?? I am interested in hearing more about it.. Thanks very much..
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Bini Ramachandran @itsbinir.bsky.social · 17/06/2026
🤣🤣 That's a good one..
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Bini Ramachandran @itsbinir.bsky.social · 17/06/2026
What is the magic soup in the PreOmics iST kit, I wonder.. It is getting me 6000 proteins from tiny FFPE samples!! Whereas the conventional workflow is hardly touching 1000 proteins!!
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Roland Pease @peaseroland.bsky.social · 16/06/2026
Another UK chemistry department in trouble - this time Sheffield. savesheffieldchemistry.netlify.app
savesheffieldchemistry.netlify.app
An Open Letter
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Bini Ramachandran @itsbinir.bsky.social · 15/06/2026
Thank you so very much.. This is exactly what I was looking for.. 😊
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Bini Ramachandran @itsbinir.bsky.social · 12/06/2026
Thanks.. was hoping for an option in Spectronaut itself rather than a downstream intervention..
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Bini Ramachandran @itsbinir.bsky.social · 11/06/2026
Is there any option to remove the contaminant proteins prior to normalisation in #Spectronaut?? Essentially, I would like to identify them, but don't want to include their abundance values for cross run normalisation.. is there a possibility?? Thanks very much..
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Bini Ramachandran @itsbinir.bsky.social · 06/05/2026
The probe can be used to analyze contents in a coffee mug, an urn, etc.. 😉
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Bini Ramachandran @itsbinir.bsky.social · 01/04/2026
Hello #Spectronaut users and manufacturers.. Is there any option to export both the raw and normalized PG.Quantity values?? Is it not possible at all or am I missing something here?? Thanks very much..
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Bini Ramachandran @itsbinir.bsky.social · 24/03/2026
Computational proteomics is cool.. Even if it is not solely proteomics.. All the very best with the new role..
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Bini Ramachandran @itsbinir.bsky.social · 24/03/2026
Link is not working for registration.. Please share a working link.. thanks..
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PastelBio @pastelbio.bsky.social · 19/03/2026
A nature-inspired ion trap for parallel manipulation of ions on a massive scale www.science.org/doi/... --- #proteomics #prot-paper
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Bini Ramachandran @itsbinir.bsky.social · 18/03/2026
There are a bunch of carboxylases which are naturally biotinylated and get copurified in streptavidin affinity pulldowns..
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Bini Ramachandran @itsbinir.bsky.social · 17/03/2026
Would this protocol require removal of copurified naturally occurring biotinylated proteins as well??
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Bini Ramachandran @itsbinir.bsky.social · 17/03/2026
I second this suggestion.. The quick and easy way to remove biotin from streptavidin is boiling in laemmli buffer.. and find a way to get rid of SDS..
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Bini Ramachandran @itsbinir.bsky.social · 16/03/2026
Have you done an on-bead digestion?? If yes, the biotin remains attached to the bead.. The streptavidin-biotin binding is very strong.. One could use desthiobiotin which has low binding affinity and hence can be eluted out of streptavidin..
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Franck Pichaud @fpichaud.bsky.social · 16/03/2026
Wow! www.nature.com/articles/s41... Here we report all five canonical nucleobases—purines (adenine and guanine) and pyrimidines (cytosine, thymine and uracil)—in samples returned from the C-type asteroid (162173) Ryugu
nature.com
A complete set of canonical nucleobases in the carbonaceous asteroid (162173) Ryugu - Nature Astronomy
Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T and U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to...
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Bini Ramachandran @itsbinir.bsky.social · 13/03/2026
Can casanovo build a spectral library from de Novo search results??
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