Thursday, October 26, 2017

TMT-C+ A simple method to improve MS2-based reporter ion quan?

This is new study at bioRXiV is worth taking a look at if you're doing MS2 based reporter quan! 

The MS3-based reporter ion quan methods on tribrid Orbitrap systems make use of the fact that there are relatively large MS/MS fragments that still possess tagged regions when fragmented at lower energy.  A bunch of those are isolated together and fragmented at extremely high energy to get a ton of reporter ions at once.

In MS-2 based reporter ion quan, we hit the tagged peptides with medium level collision energy so we can get enough information to quantify the peptide and identify it in a single spectrum. In addition to the free reporter ions in the <132 m/z range, you'll often see fragments with complementary information. For example, fragments of peptides that are also quantifiable. These have been referred to as TMTc fragment ions (C stands for complement/ary)

The IMP-Hyperplex node ( permits you to utilize these to improve your quan by adding in the TMTc ratios into the reporter ion ones and is an add-on for Proteome Discoverer 1.4.

TMT-C+ takes this method a step further by developing optimized sample prep and instrument parameters specifically for producing stronger TMTc signals. I'm unclear on the second part, but by integrating the modeling of the isolation window into their calculations (?) they dramatically improve the precision of their measurements!

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