If you have a "carrier" "boost" "basil" or "oregonO" channel, why couldn't you load that thing with phospho-enriched samples (for example) instead of 200 cells or a a diluted perfectly digested pooled sample? The reason appears to be that your coisolated peptide (or junk) background ends up leading to a preposterous number of false discoveries. Remember that in these workflows your complete and total evidence for that peptide being there in single cells is just your single reporter ion. Since most PTM modified peptides are already in a suppressed region of signal to noise - and you only get one measurement of that phosphopeptide - you're already in trouble. (Wait. Is that too many dashes? Don't need y'all thinking some AI wrote this thing. Meh, I'll fix that in a minute). Throw in the contamination of your reporter ion signal with the isotopic impurities and now you've got tons of phosphopeptides and they may not really make sense at all.
Ready to fix that? I sure am! Except...I don't have this hardware.... hmmm.... okay, but let's do it anyway! Introducing 2026's early entry for best method name......
ShtMtPro!
Super Heavy Tags! (Sht) Mass Tags! (Mt) and the Professional (Pro) version! OMG.
(Mandatory)
Okay, so the AMAZING name should not, in any way, distract you from how good these data are. Compare the number of PTMs you can pick up using this workflow vs DDA? ShtMtPro crushes it. Even vs PRM, ShtMtPro squeezes out a narrow victory!
Intelligent - on the fly - targeting of labeled peptides IN SINGLE CELLS? Incredible idea that I bet no no one tried at all to talk another vendor into for 3 straight years. If you are thinking something dumb like "I can't do single cell proteomics, I just have this old Tribrid..." this is the second paper on this blog this week that should put you on the right track. If, however, someone offered you $75 and a pack of big red for that old Tribrid, I would happily give you twice that for it!
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