Wednesday, February 8, 2012

Orbitrap Velos ETD vs. Orbitrap XL ETD

So, I've been using the new Orbitrap Velos plus ETD for about 2 months now and these are my observations in comparison to my trusty old Orbitrap XL plus ETD.
1) The shorter ion transfer tubes on the Velos get fouled about 4 times as fast as the longer ones on the XL
2) The file sizes on the Velos are approximately 1.5 times larger for the same sample as the same sample ran on the XL
3) While the number of proteins ID'ed on the Velos don't seem to exceed those of the XL, the individual peptide scores (and thus the total protein scores) are higher when ran on Proteome Discoverer 1.2
4) Although the XL plus ETD is supposed to have the same HCD cell as the Velos plus ETD, I have experienced dramatically better HCD response.  For example, I always found that the XL wasn't all that great with reporter ions such as iTRAQ and TMT, where these technologies work extraordinarily well on the Velos.
Hopefully I'll be able to run some samples side-by-side on the two machines in the near future and see how the coverage and peptide scores differ!

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