library match spectrum

library match spectrum stephen swatkoski  2019-04-02


When analyzing PRM data, is there a way to determine which replicate the library match spectrum came from? Also, is there a way to determine the exact scan number of the library match?


Brendan MacLean responded:  2019-04-03

Hi Steve,
With PRM data, you should get multiple library matches for every peptide and those should be listed in a dropdown list at the top of the Library Match view. The only ways I know that you can tell which file and at least the retention time of the matched spectrum are:

  • Looking for which ID annotation is highlighted in red when you have the matched spectrum itself selected and not one of the other spectra in the dropdown list, which will all list their replicate and retention time in the dropdown.
  • Using the View > Spectral Libraries explorer. Then every peptide you select will show the file and retention time it came from. And you can type out a peptide prefix to find a peptide in this view.

I know, not up to our usual standard of information accessibility, but that is all I can think of.

Thanks for bringing it up on the support board.