Monday, November 5, 2018

MaxQuant.Live corrections on the TopN functionality!

Some important corrections from my recent extremely sleep-deprived posts regarding my super high speed Q Exactive HF.

1) Currently, I don't seem to be able to set any resolution that I want for MS1 scans using the TopN or EASI-TAG functionalities added to my HF.  Especially for TopN, I need to set a resolution for MS1 that matches the resolution in my MS1 scan in my normal vendor software --

Yeah -- I was pretty sad about this one. I really really wanted to run my MS1 scans at 867530.9 resolution, but I can't --not in TopN -- sorry Jenny....(mandatory link)

2) I can't hit HF-X speeds with an HF. One of the coolest things about the HF-X is the ridiculous improvement in overhead time versus the older systems (down from >14ms on the QE Classic to somewhere around 3ms on the HF-X. The HF falls in the middle somewhere, the math is on this blog somewhere, but it's a lot more than 3ms. If I try to run at 8,000 resolution the amount of time it takes to collect enough ions to see + overhead does take a big toll on my overall cycle time.

The record today was around 28 Hz. Still a little better than the 22 Hz the HF normally gets, but a far cry from 41.3Hz.  I'll keep tinkering, but it is quite possible that I'm within the margin of error and I'm not actually running realistically faster than with the factory software.

3) Don't hit the stop button in Xcalibur! You'll need to close everything and start over to get the MaxQuant.Live, Xcalibur, SleasyNano handshake thing to all happen right again.

4) Super cool thing that I'm not sure how to use, but I successfully ran MaxQuant.Live from the Tune page. could realistically do a direct infusion experiment and run BoxCars on it. Calling Glaros lab -- want to write some super sophisticated methods for your PaperSpray contraptions? We might be able to BoxCar and set the new sensitivity record for direct injection. I'm also thinking FIA (flow injection analysis) is something that could gain TONS from BoxCar.

5) Did I have a point to this? I forget. Probably not!

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