Analyzing PRM raw data files for small molecules

Analyzing PRM raw data files for small molecules ssah9  2019-07-03


When working with PRM data, how do I make a transition list for multiple precursor-ion pairs? I followed the instructions given in the small molecule data tutorial and changed my settings according to the tutorial on targeted MS/MS data. I am not sure if that's how I should go about analyzing my prm files. the data is from a thermos qexactive


Brendan MacLean responded:  2019-07-03

Hi Samyukta,
Any chance you could provide a screenshot of your Targets list. It is hard to follow what you are trying to achieve. Are you working with small molecules or peptides? If you are working with peptides then Webinar 17 ( may be helpful.

Have you imported any PRM data yet? How does that look?


Brendan MacLean responded:  2019-07-03

So, are you asking whether you can have multiple products per precursor? or just multiple precursors each with their own product? The answer to both is yes. I am not sure, though, why this is not clear from Skyline tutorials and material in general.

I am probably still not understanding something, because I have a hard time seeing how this could be a question: "if I could have multiple precursor-product ion pairs in one file"

You did this for just one fragment of one precursor? Even the small molecule quant tutorials has 2 precursors and the others have many.

Is it the PRM part that is confusing you? Since most of the small molecule tutorials use SRM?

Anyway, it is possible and highly recommended.