1) has some of the prettiest plots I've ever seen for proteomics data
2) started in a completely different and really smart way to work out carrier channel ratio compression (using swapping TMT126 chanel for TMT0 to get some sense of ground truth.)
And what's really impressive is how consistent every study that has looked at using amplification via (SCoPE-MS or BOOST or whatever terminology this all lands on in the end) has been in the end. Now, this is the most conservative estimate to date, but everything has been pretty much in the same ballpark. There is a single order of magnitude between the lowest estimate and the highest, we're somewhere between 20 and 200).
Always worth considering here, and I apologize if I'm starting to sounds like a broken record (whatever that means) but every study so far has been on an Orbitrap, with only one group using the bigger D30 Orbitrap and everything else using the D20. Not to oversimplify the physics involved, but it's not just coincidental that the larger Orbitrap measurements have biased toward higher carrier.
We've known all along that while the Orbitrap is one of the single most awesome things that has ever been invented, the instrascan linear dynamic range is NOT why you buy one. You want big instrascan dynamic range that's linear? Get a QQQ. Everything else falls in the middle.
Back to the paper:
Another really good paper I'll be referencing all the time has done the carrier ratio suppression math and just to flag why I'm so impressed by them getting to the same conclusions:
We're a 20+ year old field and not one single one of us can digest a sample the same way. Proof in point?
Paper earlier this year?
1:50 trypsin with overnight digestion at room temperature
10mM DTT for 30 min at 56C
55mM IAA for 45 min at RT
Some other changes:
In Claudia's new paper we see something slightly different (surprise)
1:100 trypsin overnight at 37C
50mM DTT for 30 min at 37C
40mM IAA at room temp for 30 min
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