Question: pathway analysis of differential expressions
gravatar for robjohn70000
4.3 years ago by
robjohn70000120 wrote:


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.


mass spectrometry R proteomics • 1.1k views
ADD COMMENTlink modified 4.3 years ago by Jean-Karim Heriche21k • written 4.3 years ago by robjohn70000120
gravatar for Jean-Karim Heriche
4.3 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

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.

ADD COMMENTlink written 4.3 years ago by Jean-Karim Heriche21k
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