Saturday, June 1, 2019

Finally! More instrument methods for!!

HAPPY ASMS EVERYONE!!! If you aren't here, don't worry, I am. And I plan for zero sleep and 400% productivity. As proof -- I gave myself a deadline. Today. For new ready-to-go instrument methods.

You can get them at or you can get them directly from the GitHub account here. (Click on the ASMS 2019 Update Zip file and it will take you to a page with a download button.)

What's in there?  How 'bout 107 new methods? That's a lie actually, many methods were just opened and checked for compatibility in Exactive Tune 2.11 to verify they worked properly. But there is a lot of

MaxQuant.Live is awesome, and once you use it a couple of times to get the hang of it you'll find it really easy to give your HF or HF-X some super powers. There is a folder containing both the Xcalibur and MaxQuant.Live methods properly linked. You'll just need to add your chromatography conditions and go.  I threw in the super speed method for the HF (run it at HF-X type speed -- but, be warned, due to the higher overhead, it doesn't perform as well as the HF-X). There are also some premade BoxCar methods.

Speaking of BoxCar stuff, I get loads of questions about running BoxCar like methods on the Fusion and Lumos. The Tribrid methods that come premade are AMAZING, so I haven't felt it necessary to release stuff for these systems, but I've thrown in my BoxCar iterations (built in Lumos with tune 3.1). I've also included some notes on the methods and things to help make sense of it.  Here are my definitions, though

BoxFahrt -- kinda like BoxCar, but not quite as powerful as MaxQuant.Live BoxCar

BoxCar Assisted MS/MS Fragmentation (BAMF) -- like BoxCar, but the ions selected for MS/MS are selected FROM the BoxCar scans rather than the MS1.

BoxCarDIA -- Utilizing the ion trap to do small DIA windows while the slow BoxCar scans are happening. I have files, but I haven't found any way to process the data. Want to give it a shot? Shoot me an email. I'll get you files from this Lumos I get to play with! My goal is to use the low res DIA for confirmation only (similar to WiSIMDIA)

Methods for the Exactives without Quads -- (Exactive Plus and Plus EMR) -- including multi-"phase" methods I've been developing on mine in Columbia. Proteins can be dumb about ionizing. One antibody might need 50 SID to ionize and the next 80 EV. By utilizing the "advantage"(?) of wide peaks for intact proteins, you can have multiple methods with different methods in a single peak and more rapidly figure out the ideal settings for that protein.

I'm doing a lot of work with pesticides these days -- my daily method for rapid pesticide screening with confirmation MS/MS for QE Classic.

What didn't make the cut?   Triple quad methods (I've got a TON of good ones, particularly for metabolites and pesticides!), Peptidomics. Lipids. Crosslinking on the Q Exactives, but it's some progress, at least!

1 comment:

  1. Great resources, thanks a lot, however having trouble to open the Tribrids methods (what Xcal version are you using ? we have the 4.1) if possible to have the methods in other format (Print as XPS file for example).