How to relate Spectrum Title to Retention Time?

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Lee S Parsons

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Aug 25, 2016, 3:46:02 PM8/25/16
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I used DeNovoGUI 1.12.2 to examine two spectra that I exported to MGF from Thermo .raw (orbitrap instrument) using msconvert.  My goal in this analysis is to get the retention times of the detected peptides but I cannot find it in the exported files from DeNovoGUI.  I exported the peptide matches (Export -> Peptide Matches) and I see Spectrum Titles such as "LSP_stdB.4200.4200.2".  I originally thought this was a value in seconds, however I see there are some that equate to times well beyond the length of the gradient. 

I checked my MGF files and in there I do see the "RTINSECONDS" line for each spectra, and in there I see reasonable time values. 

Is there a way to convert the numeric part of these Spectrum Titles to the Retention Time for these spectra?  Or is there another way to get the retention data in relation to the best peptide matches?  If I look in the .novor files for example, I see useful retention time values (in minutes in this case which is fine) but I would prefer to see a single file for all the searches I used in this job.

thank you
Lee

Marc Vaudel

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Aug 25, 2016, 4:12:45 PM8/25/16
to Lee S Parsons, DeNovoGUI
Hi Lee,

If I remember correctly the number in the spectrum title corresponds to the index of acquisition. I think the easiest would be that we include it to the export. I will look into it and come back to you.

Best regards,

Marc


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Lee S Parsons

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Aug 25, 2016, 4:47:37 PM8/25/16
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Thank you for the quick reply Marc!

When I look at the results in DeNovoGUI I do see valid RT values there as well, they just aren't exported any place that I can see. 

If it helps, what I would like to be able to do is export a table that would have (file) (spectra title) (RT) (m/z) (sequence) (score).  For what I'm doing with this right now I don't need the rest.  If I could get that for all the matched spectra that would be great, I can sort it out later.  If I could say something like "all the spectra that gave a sequence at least X AAs long with a score better than Y" that would be great as well. 

Although I could even extract all that from just exporting everything that is displayed in the DeNovoGUI results that I see on my screen; I just don't seem to have a way to do that. 

thank you
Lee
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Harald Barsnes

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Sep 12, 2016, 10:10:46 AM9/12/16
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Hi Lee,

We've just released DeNovoGUI v1.12.4 which adds retention time to the exports. Hopefully this will give you want you need.

Best regards,
Harald
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