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 On Tuesday, November 14, 2023 at 4:35:55 PM UTC-5 Jimmy Eng wrote:
> 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. > > On Tue, Nov 14, 2023 at 1:17 PM Iryna Abramchuk <[email protected]> > wrote: > >> 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! >> >> On Tuesday, November 14, 2023 at 3:46:34 PM UTC-5 Jimmy Eng wrote: >> >>> 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. >>> >>> On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk <[email protected]> >>> wrote: >>> >>>> Thank you! Do you know if there is any way to extract the precursor >>>> peak intensity with XPRESS (or other TPP tools)? >>>> >>>> On Tuesday, November 7, 2023 at 4:32:25 PM UTC-5 Jimmy Eng wrote: >>>> >>>>> "peak_intensity" is the maximum peak intensity of the ion chromatogram. >>>>> >>>>> On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk <[email protected]> >>>>> wrote: >>>>> >>>>>> 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 >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "spctools-discuss" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to [email protected]. >>>>>> To view this discussion on the web visit >>>>>> https://groups.google.com/d/msgid/spctools-discuss/ea66065e-0b21-43cd-9f00-703ad9e8d3f7n%40googlegroups.com >>>>>> >>>>>> <https://groups.google.com/d/msgid/spctools-discuss/ea66065e-0b21-43cd-9f00-703ad9e8d3f7n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>> . >>>>>> >>>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> >>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/spctools-discuss/9c3553a8-a00d-4e0b-97f1-065b7171f0c6n%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/spctools-discuss/9c3553a8-a00d-4e0b-97f1-065b7171f0c6n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/604ac869-61a1-462a-8a5c-cc84890e133fn%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/604ac869-61a1-462a-8a5c-cc84890e133fn%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/dff91f30-f32b-4ba0-8e69-fcc63e7f2880n%40googlegroups.com.
