Honestly, it was a bit of miscommunication between a friend and I that ended up in finding out that this works. And...besides the application we were discussing (which is secret) I can't think of a reason off the top of my head that this would be useful...but...
If you did have some cool PSMs that you were interested in --- wait -- I've got one! Okay. So..what if you found some PSMs that were differentially regulated but you wanted to see if all the ones that looked significant were possibly contamination. Then you could do this!
Use your filters to reduce your PSMs (or MS/MS spectrum input or whatever) down to the list you are interested in and checkmark them. (You can highlight a whole big group and then tell it to "Check selected").
Then you can go up to export and export out the spectra in any of the PD supported formats. In this case, we did mZmL.
Then you can reimport that mZmL as an input file.
And then run this smaller file through your pipeline with that contaminating organism database!
Thank you for this, this is the exact thing I needed to be able to do, for, um reasons.... :)
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