Using Crux toolkit on SILAC data

[Caroline Labelle]

Hello,

We are currently using the Crux toolkit in a course in which we are introducing students to mass spectrometry data analysis. The documentation is complete and well written, and the tools are easy to use!

We would like to use Crux on SILAC data, but we are not sure if this is possible. In the FAQ there are examples of how to search isotopically labelled data: we used that information to do a tide-search, but it is not clear how we can compare heavy/light samples after that. 

Would it be possible to have some guidance or some tips on how (and if) we can use Crux on SILAC data?

Thank you in advance!

Caroline

[William Stafford Noble]

Hi Caroline,

I am glad to hear that the Crux software is working for you. The example from the FAQ only shows how to search SILAC data. Unfortunately, we don't have any tools within Crux directly to actually extract the corresponding quantitative values from SILAC data. One could, for example, do this with a spectral counting approach or using MS1 peak areas. The former would be the most straightforward. You would simply need to segregate your spectral counts based on the presence of absence of the corresponding variable modification.

Bill