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Mutant vs Control protein expression ratios

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Mutant vs Control protein expression ratios oo254  2015-11-18 15:20
Status: Closed
 
Hi,

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
Hello,

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:

https://www.labkey.org/wiki/home/Documentation/page.view?name=quantitation

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

https://www.labkey.org/wiki/home/Documentation/page.view?name=spectraCount

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

https://www.labkey.org/wiki/home/Documentation/page.view?name=ms1Pipelines

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:

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorials

https://panoramaweb.org/labkey/wiki/home/page.view?name=Importing%20data%20into%20Panorama

Thanks,
Josh