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pathway analysis of differential expressions

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

mass-spectrometry r proteomics
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updated by Ram Ram • written by robjohn70000 robjohn70000

1 answer

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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written by Jean-Karim Heriche Jean-Karim Heriche

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