pathway analysis of differential expressions
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6.1 years ago
robjohn70000 ▴ 130

Hi,

I'm new to proteomics and need to analyze some ".mzML" data obtained form LTQ Orbitrap Velos. I will like to  find perturbed pathways based on the differential expressions of  mutant/wild-type(control). Does anyone know what steps are necessary to do this kind of analysis either in R or another platform. In particular I'm not sure what aspects of the ".mzML" data I would need for the analtsis.

Thanks

R proteomics mass spectrometry • 1.4k views
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Entering edit mode
6.1 years ago

You need to run a peptide/protein identification software on the spectra contained in your mzML files. There are different software with different approaches. For a free, open source solution, have a look at the Trans-Proteomic Pipeline.

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