Friday, May 18, 2018

Addressing more BoxCar/BoxFahrt comments!

It can be hard to both post and to find comments that are made on this dumb blog. Especially when they go on separate posts. It helps to address them directly sometimes! In no particular order

Q1) Is the Xcalibur add-in available yet?

--Not yet, I don't think. I'll probably run around screaming when I find out it has

Q2) How can you process the data currently?

-- For the TMT stuff we've been doing (LFQ runs are on this weekend when I did the math and realized there were a few (very rare in our lab) open hours on something!) Proteome Discoverer 2.1 has no problems with the data. Actually -- I know the peptide ID is great, but I need to do the quan comparisons later. I haven't tested PD 2.2 (I'm using IMP-PD nodes for this project and they aren't all available in PD 2.2 yet)

-- The MaxQuant version in the BoxCar paper is specifically equipped for real BoxCar data. I don't know yet (maybe next week) if it can handle BoxFahrt.

-- Testing is in progress right now for RAWQuant --- which, honestly, deserves it's own post. It's REALLY cool and I think it is something that we need to integrate into our data processing immmediately.

NOT A Q!!!)  Okay -- so -- thank you Chris -- I didn't know that the Fusion has features to allow you to select individual isolation windows. I will evaluate this immediately.  If you can optimize your isolation windows to spread out the densest regions of ion current (like BoxCar does) -- the results I'm getting on the Fusion right now might just be the beginning of the improvements I'm seeing!!

Q3) How does this differ from WiSIMDIA? It's got some similarities in that we're doing gas phase fractionation for the MS1 -- and WiSIMDIA is probably a good starting template for how BoxCar can be adapted to DIA. BoxCar staggers the isolation in the MS1 and allows for a more even distribution of MS1 ions than WiSIM -- and that even distribution allows lower intensity ions to come up out of the noise and be selected for fragmentation.

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