Saturday, March 1, 2014

Blogger hates histograms -- or a study on the distribution of ions selected for fragmentation on an Orbitrap

 Whats this weird thing, you ask?  Well, this is a histogram.  And blogger apparently hates histograms, cause I've tried everything and this is the only way it will display.

Misconception?  If we digest a whole cell lysate with trypsin, we will find that there is an apex somewhere which will represent the average tryptic peptide mass as well as the standard distribution around that point.

So I took a HeLa digest run.  We know its well over 90% digested, so it should be a good comparison.  I then filtered every the m/z of every ion that was selected for fragmentation by a filter of 0.01 Da.  This provided me with 10,979 unique-ish ions selected for fragmentation.

In order to get a visual output representing the ion distribution, I binned the ions in 1 Da units from 299 to 1000.  And I got this neat histogram that appears to show little m/z bias (so no obvious apex and distribution!)

 But it sure is hard to see, right?  So I just re-binned it in units of 50.  Which shows some bias, but definitely not as strong as I was suspecting.

I'm surprised and not real sure what to make of this.  In particular due to groups that are using predictions of peptide distribution for pre- and post- processing analysis.  Gonna have to do some reading, but for now, I'm off to:

I can't say the blog is on hiatus, but maybe!

BTW, these histograms were created by the Add-in in Office 365, which is pretty great.

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