XPRESS peak intensity value

[Iryna Abramchuk]

Hello all!

I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the "peak_intensity" output value. I was just looking to confirm whether "peak_intensity" is the precursor peak intensity, or if it's the maximum peak intensity of the ion chromatogram?

Thank you

[Jimmy Eng]

"peak_intensity" is the maximum peak intensity of the ion chromatogram.

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[Iryna Abramchuk]

Thank you! Do you know if there is any way to extract the precursor peak intensity with XPRESS (or other TPP tools)? 

[Jimmy Eng]

I might need some clarification on what you're asking as XPRESS (and possibly the other quant tools) does extract the precursor peak intensity and area.  And if you just want the peak area for peptide IDs and your sample isn't isotope labeled, run it in label-free mode where it will simply pull out the peak area/intensity for each peptide/precursor. 

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[David Shteynberg]

Hello Iryna,

The xinteract tool in the TPP, accessed in Petunia interface in [TPP Tools] -> [Analyze peptides]) , the option -PREC can be specified in the [PeptideProphet Options] -> [Enter additional options to pass directly to the command-line (expert use only!)].  This option will record precursor_intensity for each PSM in the pepXML file.  You can then add this column in PepXMLViewer and it should be populated with parent intensities from the mzML file.

Cheers!

-David

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[Iryna Abramchuk]

I am using XPRESS in label-free mode and at the moment I am seeing peak_intensity (which I understand is the maximum peak intensity of the ion chromatogram) among other outputs. I am looking for the precursor intensity though, which I do not see.

I think David's answer is what I was looking for (adding the -PREC option to get the precursor_intensity). Thank you for your help! 

[Iryna Abramchuk]

Awesome, thank you so much! 

[Jimmy Eng]

Hopefully you get what you need from David's response.  But just to clarify, XPRESS writes out both peak_intensity and peak_area when it runs.  So if you do see the "peak_intensity" column in the pepXML Viewer, go to the "Pick Columns" tab  and select "peak_area" as a column to display.  More than anything, I'm just curious if you are able to display the precursor "peak_area" by selecting that column with your existing analysis.

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/604ac869-61a1-462a-8a5c-cc84890e133fn%40googlegroups.com.

[Iryna Abramchuk]

Yes, I do see both peak_intensity and peak_area as XPRESS outputs in the XML files, and can also view these columns in the PepXML viewer

[sudarshan kumar]

Do we have any dedicated discussion group for SILAC using aspartio and express?