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 On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk <iryna.abra...@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-discuss+unsubscr...@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/CAGJJY%3D8YDDDw23fiz3GrO0pc-H27Lf%2BQjXxJV_1648goXY8RTQ%40mail.gmail.com.
