Ron Beavis recently reminded me that the the GPM has several very useful graphs that are automatically created when you search your data using theGPM
The Graph below plots the fraction of identified spectra (Green) plotted against the predicted retention time in %ACN. How it converts this to %ACN will hopefully be posted shortly in an edit
As you can see the Green dots follow the line you expect them to follow if they are in fact true identifications. That is, they follow the gradient that peptides usually follow
This next example does not follow the expected gradient and is most likely comprised of false identifications
Pretty easy way to determine the quality of your dataset right? It is also very useful for diagnosing problems with your LC system such as a big delay volume.
The GPM is updated regularly, so it’s worth checking every so often for more goodies the GPM folks add. They are not very good at advertising however so these features are easy to miss.
Update (Oct 1-2014)
Ron has made a much more in-depth explanation of this than I did. Please head over to thegpm to check it out