One of the most important benefits of the quantify-then-identify approach we use in Progenesis LC-MS is that you can find the significantly changing features even when you have no MS/MS data to identify them. Paddy talked about this a few months ago after giving his presentation at the London Biological Mass Spec Discussion Group.
To show how this works when you’re actually using the software, we’ve added a new video to the Progenesis LC-MS section demonstrating the quantify-then-identify approach with targeted inclusion lists. This lets you gather more MS/MS data after quantification of MS1 data, so you have more chance of getting identifications for the features that you’re interested in — even if they were missed previously.
Watch the video now, so you can see how this works. You’ll also get a peek at some of the new tagging features coming soon in Progenesis LC-MS v3.0.