Thursday, November 29, 2018

Last QE Turbo post, for real!

This might be the last one. (Continuation of this post, possibly yesterday? I forget)

What if the fill times were exactly the same on a QE HF running the same method and the same fill times (arbitrarily 30ms, cause why not?) and all I changed was the MS/MS resolution? 15k vs 8k?

You'd expect to get more scans when using 8k MS/MS, right? Because you'd definitely get more scans completed when you didn't need the full fill time.  More scans = more peptides!

I had a small opening overnight so I put on 500ng of HeLa and ran it on a 45 minute gradient 4 times.
2x with 60k res MS1/15k res MS/MS with top 30 and 30ms max fill time
2x with same except 8k res MS/MS

With 15k MS/MS -- 46,900 and 46,978 MS/MS scans
With 8k MS/MS -- 54,012 and 53,606 MS/MS scans

14% more MS/MS scans! WOOHOO!!

Then it gets less cool.

Clearly this is pseudo-pscientific, but it doesn't appear that my HF benefits from running MS/MS at 8,000 resolution. Honestly -- this is about what I'm seeing on the Fusion 1, to the point I don't use a transient below 15,000 resolution. I would like to take this apart. Like -- where are those 7,000 extra MS/MS scans going? Does mass accuracy appear to suffer due to peak coalescence at the lower resolution? That seems the most likely explanation, but no time to investigate right now.

This is good for me, probably. There was this increasing temptation to use MaxQuant.Live to "hack" my instrument every time there was a gap in the queue, but with this kinda settled, it's time to get back to the metabolomics!!

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