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 <iryna.abra...@gmail.com> 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 <iryna....@gmail.com> >> 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 <iryna....@gmail.com> >>>> 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 spctools-discu...@googlegroups.com. >>>>> 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 spctools-discu...@googlegroups.com. >>> >> 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 spctools-discuss+unsubscr...@googlegroups.com. > 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAJqD6ENe%2Bqta80w3QHKJbTYWUjQGi%2BBnQdEXYQ367CkedmAq9w%40mail.gmail.com.
