Mutant vs Control protein expression ratios

Installation Forum (Inactive)
Mutant vs Control protein expression ratios oo254  2015-11-18 15:20
Status: Closed

I have been playing around with some ".mzXML" data obtained from "LTQ Orbitrap Velos" raw data on the LabKey server. I will like to find perturbed pathways based on the differential expressions of mutant/wild-type(control). Even though I have followed the tutorials in the LabKey documentation, I'm still not sure about the steps that are necessary to do this kind of analysis that I'm interested in. For example, I need to know which proteins are over/under- expressed in either mutant or the control. How can I use LabKey server to achieve this? Any help will be appreciated. Thanks
jeckels responded:  2015-11-21 17:33

This greatly depends on what your data looks like.

If you have isotopically labeled the samples, you can use one of the supported quantitation engines when you do a protein database search:

If you have analyzed the samples separately, you could use a spectra counting approach:

or you could use MS1 feature data for quantitation purposes, with the "msInspect Feature Peptide Matching Analysis" pipeline:

However, if you're doing DIA, you would likely want to use Skyline to analyze the data and then import into Panorama within LabKey Server: