Keshava Datta, Ph.D.

Bottom-up #Proteomics guy helping biologists with their LC-MS experiments... #TeamMassSpec

[Keshava Datta, Ph.D. @Keshava_Datta]

@jjjotto @mswilbv If using micros at that throughput, I'd use the plate format.

[Proteomics Daily News @Proteomicslabo]

🔬 CoPISA enables high-throughput profiling of protein solubility changes induced by drug combinations.
🔗 https://t.co/M1tDNad67v
#Proteomics #MassSpec

[bioRxiv Neuroscience @biorxiv_neursci]

A Deep Quantitative Proteome Turnover Platform for Human iPSC-derived Neurons https://t.co/MlDQaXY6xx #biorxiv_neursci

[Chandra R. Srikanth @chandrarsrikant]

Context and possibilities

When your dad is a partner in a private equity fund or running a family office in West Asia or you grow up having a millionaire uncle, your context is completely different.

Your context does not limit your possibilities.

The schools you go to, the college hostels you are in, the kids you befriend at functions, the restaurants you eat at, the clubs you play tennis and golf in, among other things seen and unseen.

While a person without these factors dithers about even knocking on a door, the privileged one opens the door with flair and struts right in.

It's not unfair, it's just a fact of life.

#Musings

[Nassim Nicholas Taleb's Wisdom @TalebWisdom]

"If you do not take risks for your ideas you are nothing. Nothing." - Nassim Nicholas Taleb #risk

[Keshava Datta, Ph.D. @Keshava_Datta]

The real question is: Do you actually quantify your peptides before they hit the autosampler, or are you just "winging it" and hoping for the best? 😉

#Proteomics #MassSpectrometry #LCMS #Chromatography #Bioanalysis

[Keshava Datta, Ph.D. @Keshava_Datta]

“Just load more” is the biggest lie in Proteomics!

We’ve all heard it - When they don't find their favorite protein: "Just increase the injection volume."

Tell you what, more is not always better... Okay, maybe except for when it’s your paycheck 💸

[Keshava Datta, Ph.D. @Keshava_Datta]

❌ Space-Charge Effects: Pushing too many ions at once doesn't give better data!

Optimizing injection amount is a balancing act. One has to weigh:
✅ Column ID & Length
✅ Flow rates & Gradient duration
✅ Mass Spec scan speed

[Keshava Datta, Ph.D. @Keshava_Datta]

The result of a "sick" Trypsin: Ion suppression, vanishing sensitivity, and a lot of wasted instrument time.

What’s your "secret sauce" for a near 100% efficient digestion? 💡

#MassSpectrometry #AnalyticalChemistry #Proteomics #ProteinChemistry #LabTips

[Keshava Datta, Ph.D. @Keshava_Datta]

Did your Trypsin take a sick day? 🤒

We often obsess over mass accuracy and scan speed, but the most sophisticated mass spec in the world can't fix a failed Trypsin digestion.

The attached spectrum is a textbook example of Undigested Protein.

[Keshava Datta, Ph.D. @Keshava_Datta]

If your spectra look like this, it’s time to audit:
✅ Buffer pH: Is it still between 7.5 and 8.5?
✅ Urea concentration: Is it diluted enough (<2M) to keep Trypsin active?
✅ Detergent removal: Did residual SDS kill the enzyme?
✅ Trypsin Quality: Stock older than your PhD?

[Keshava Datta, Ph.D. @Keshava_Datta]

Garbage in, Gaussian polymers out.

How long did it take you to scrub your LC-MS system after the last time you got "PEG-ged"?

#MassSpectrometry #Proteomics #LabLife #AnalyticalChemistry #Orbitrap

[Keshava Datta, Ph.D. @Keshava_Datta]

Have you ever been "PEG-ged"? 🫣

No, not that. Get your mind out of the gutter... I’m talking about the 44 Da Headache.

You check your TIC, expecting beautiful, complex, peptide envelopes, but instead, you see this: a perfect, rhythmic "mountain range" mocking you.

[Keshava Datta, Ph.D. @Keshava_Datta]

Detergents: 🧼 Triton-X or Tween-20 that wasn't cleaned up
The Human Element🧴: Hand cream or hair products (Wear your gloves, for Orbitrap’s sake!)

The reality: You can have the most expensive mass spec in the world, but your data is only as good as your sample prep.

[Keshava Datta, Ph.D. @Keshava_Datta]

Do you prioritize speed, recovery, or cost-effectiveness?

#Proteomics #MassSpec

[Keshava Datta, Ph.D. @Keshava_Datta]

Which Proteomics Protocol Wins Your Vote?

Unlike fields such as genomics, proteomics is uniquely challenging because there isn't a single "universal" protocol. Different labs and facilities utilize various methodologies — each with its own advantages and limitations.

[Keshava Datta, Ph.D. @Keshava_Datta]

There's FASP, S-TRAP, SP3, PAC, and enough other abbreviations to fill a dictionary!

Thankfully, some groups have done the ground work by comparing these methods in parallel. This study is a personal favorite: https://t.co/ONXkm6ArmW

Which acronym is your daily driver?