For some time now, PepNovo+ has included a rank score for ranking PSMs in addition to the PepNovo score. This score, as detailed in Frank (2009), is significantly better at selecting between PSMs for a given spectrum. Currently DeNovoGUI ranks PepNovo+ results within each spectrum by PepNovo Score, not by the Rank Score. As it is now, this can result in top-ranking PSMs being excluded from results files if one is exporting fewer PSMs to a text file than were returned by the search. In the attached example, exporting the top 5 matches/spectrum would exclude the best match (by Rank Score criteria) for this spectrum.
Would you consider either 1) ranking (the "Rank" field in DeNovo GUI) PSMs within spectra by Rank Score, the better criterion, rather than PepNovo score as is done currently or 2) passing on the rank score index from .out files ("#Index") to DeNovoGUI as a separate field in addition to the current DeNovoGUI ranking? It would be helpful to have some sort of embedded ranking index based on Rank Score for each spectrum instead of/in addition to the PepNovo Score-based indexing currently present.
This is just a suggestion for a new feature if you are willing. DeNovoGUI works great as it is, but this kind of feature would save me a lot of time downstream, as I have been using Rank Score to select matches.
(Transferred from https://groups.google.com/forum/#!topic/denovogui/tk8XCRWXQ2A)
For some time now, PepNovo+ has included a rank score for ranking PSMs in addition to the PepNovo score. This score, as detailed in Frank (2009), is significantly better at selecting between PSMs for a given spectrum. Currently DeNovoGUI ranks PepNovo+ results within each spectrum by PepNovo Score, not by the Rank Score. As it is now, this can result in top-ranking PSMs being excluded from results files if one is exporting fewer PSMs to a text file than were returned by the search. In the attached example, exporting the top 5 matches/spectrum would exclude the best match (by Rank Score criteria) for this spectrum.
Would you consider either 1) ranking (the "Rank" field in DeNovo GUI) PSMs within spectra by Rank Score, the better criterion, rather than PepNovo score as is done currently or 2) passing on the rank score index from .out files ("#Index") to DeNovoGUI as a separate field in addition to the current DeNovoGUI ranking? It would be helpful to have some sort of embedded ranking index based on Rank Score for each spectrum instead of/in addition to the PepNovo Score-based indexing currently present.
This is just a suggestion for a new feature if you are willing. DeNovoGUI works great as it is, but this kind of feature would save me a lot of time downstream, as I have been using Rank Score to select matches.
Thanks, Adriana