Saturday, March 6, 2021

The best free software for protein deconvolution!


Have I posted all this before? I feel like I have, but the question comes up all the time. 

Scenario -- you have a beautiful spectra of an intact protein like the thing above and you just want the deconvoluted mass and you don't want to spend $6k for one seat of software to get something like this?


This is the NIST mAB standard with 2 clear glycoforms (148,080 Da)

If you can pick out one single peak and get one pretty spectra like the top panel, there is a software from 1998 wrapped in a nice GUI that works in Windows 7 and 10 that will do this in under 10 seconds. 

This is the paper that explains it. 

And someone, not me, put up a link to the secret word-of-mouth, you can only get at ASMS from a friend of a friend if you bring a clean USB stick and meet behind the piano bar at a specific time, GUI that contains this GUI. 

The legality of the software is something everyone always seems worried about. Everyone made me concerned enough that I've never once put up a link for it, but since someone else put up a link with the intention of mentioning it to people a lot at the 2 overlapping conferences this week (ABRF & USHUPO simultaneously? Wut?) 

You can get it here.  There is an old video from some rambly nasaly person using an older version on Vimeo that eventually shows you how to use it

Okay -- so that works for extremely simple stuff. What if your protein isn't fantastic? You can go crazy sorting through and averaging MS/MS spectra.

Here is the question you need to ask next; Do you:

1) Want to see if your protein is there? 

OR

2) Do you want to look at the difference in the proteins between sample A and sample B? 

If I answer #1, then I go straight to UniDec. 


If you answered #2 then I fire up FlashLFQ, which I find easiest to use through the Proteoform Suite.  Proteoform suite is designed for big top-down, but I'd argue that this is just as good for antibody characterization as any of the expensive software packages out there. You need to convert your files to mz(X?)mL first and then you can deconvolute all the proteins in your file and do quantitative comparisons between files. 

Angry baby, gotta go. Hope this is helpful somehow! 

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