Export "Spectrum IDs" tab

[Juan Camilo Rojas Echeverri]

First of all, AWESOME TOOL!

I am interested in answering this question: with my current instrument method, what is the minimum ion intensity that would be worth picking up for producing a useful MS spectrum?

For this purpose I want to export the information associated to all the acquired MS/MS spectra (with associated ID of whatever confidence or none) and plot Precursor intensity vs Score with hopes of finding an intensity cut-off to make my DDA methods more efficient by not wasting time in ions that will simply output a reliable spectrum for identification.

This information seems to already be imbedded in the Spectrum IDs tab but I haven't been able to find a way of exporting it.

Maybe I am missing something very obvious so could you please enlighten me?

In beforehand, thank you for your time and help.

Sincerely,

Juan Camilo

[Harald Barsnes]

Hi Juan Camilo,

If you simply want to export the content shown in the table at the top of the Spectrum IDs tab you can use the export icon to the upper right of the table (it's the one that looks like an arrow pointing upwards). This will export all the data to a tab separated text file that you can explore further in other tools.

It is also possible to right-click in a table to plot the data directly inside PeptideShaker. Not sure if it is the best option for what you want (and the feature is in a beta state), but could be worth a try. (Note that if you are plotting the Intensity vs. the Confidence you have to scale the size of the data points via clicking the Size option, as otherwise the data points will probably not be visible.)

If neither of these two options satisfy your needs, you can have a look at the customizable export options (available via Export > Identification Features), which enables you to export pretty much any value from PeptideShaker in your chosen format.

Best regards,

Harald

[Juan Camilo Rojas Echeverri]

Hi Harald,

Thank you very much for the response. I haven't noticed the export icon until you pointed it out. I was able to get the data I needed. Although I was not able to accomplish my initial objective it quickly showed there was something strange with the intensity values reported in my .mgf exports from Progenesis. The value was not the intensity of the precursor ion of the MS/MS spectrum shown, but something called "normalized abundance of the precursor ion" in the LC-MS run.

I tried before creating a customizable export that contained the intensity of the precursor but didn't find as an option that I could tick. I could only find an option for the intensity of the fragment ions.

Thanks again for the help.

JC

[Harald Barsnes]

Hi JC,

> I tried before creating a customizable export that contained the intensity of the precursor but didn't find as an option that I could tick. I could only find an option for the intensity of the fragment ions.

I think you are correct that this particular value is not available from the custom exports. Probably due to precursor intensity not being a mandatory element in mgf files. Still, I will look into it and see if we can include it in future versions.

Best regards,

Harald