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compomics / denovogui

Graphical user interface for de novo sequencing of tandem mass spectra
http://compomics.github.io/projects/denovogui.html
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pNovo Results Top 1 #48

Open lutfia95 opened 1 year ago

lutfia95 commented 1 year ago

Dear Authors,

Thank you very much for providing this nice tool. I was trying to run pNovo using your wrapper. I could successfully run the tool and produce the results. According to the user-guide from pNovo one can choose between top1 and top10 results, this case will be when I use the pNovo3_Search.exe ( I already tried to do so but the tool keeps running for hours without any progress) so I decided to use your DeNovoGUI instead. By running pNovo3 using DeNovoGUI, the produced results file are the top 10 (sample_pnovo.res.txt). Is there any setting in your GUI to produce the top1 results? The top10 results file doesn't contain aaScore and some other values, which I need for downstream analysis. Thank you very much!

Best, Ahmad

hbarsnes commented 1 year ago

Hi Ahmad,

Due to licensing issues we stopped supporting pNovo in DeNovoGUI a while back. DeNovoGUI itself is also not really maintained anymore as both Novor and DirecTag can now instead be run via SearchGUI.

With regards to controlling the number of hits per spectrum, it seems like we never properly implemented this option in DeNovoGUI. However, DeNovoGUI is basically just a wrapper around the individual de novo algorithm command lines and you can therefore simply alter the pNovo parameter file and run the command line directly.

The pNovo command line looks something like this:

pNovo3.exe pnovo_params.txt ""

An example of a pNovo parameter file can be found in the DeNovoGUI-1.16.8\resources\pNovo\windows folder after you have run pNovo once via DeNovoGUI.

All you have to do is go down towards the end of the parameter file and change

#number of peptides reported
report_pep=10

into

#number of peptides reported
report_pep=1

and then rerun the pNovo command line.

Hopefully this should give you just one hit per spectrum in the output file.

Best regards, Harald

lutfia95 commented 1 year ago

Hey Harald,

thank you very much! yes I already did that, but the tool is not able to produce the aaScores for the different amino acids. No problem, thank you very much! From my side, we can close the issue.

Best, Ahmad

hbarsnes commented 1 year ago

Hi Ahmad,

but the tool is not able to produce the aaScores for the different amino acids

Not sure which tool you are referring to here? Is this something that more recent versions of pNovo includes?

The only de novo algorithm that I know of that provides such scores is Novor.

Best regards, Harald