pathway analysis of differential expressions

Question

[robjohn70000]

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 analysis.

Thanks

Answer 1

[Jean-Karim Heriche]

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.