Great, glad that it is now working for you! We will remove references to that deprecated parameter from our documentation. Cheers, --Luis
On Fri, Sep 9, 2022 at 1:54 PM Yasir Ahmed <yazah...@gmail.com> wrote: > Thanks Eric and Luis! Turns out I was using the wrong/older syntax in the > condition file (targetMS level = “3”). The quantification works now. Thanks > for your help!!! > > Cheers, > Yasir > > On Sep 8, 2022, at 6:15 PM, 'Luis Mendoza' via spctools-discuss < > spctools-discuss@googlegroups.com> wrote: > > Hi Yasir, > Is your data Thermo SPS where the reporter ions are in MS3? If so, please > check the relevant box when producing the condition file: > > <image.png> > > > As Eric noted, it does not seem like your MS2 spectra contain reporter ion > signals, at least from the one spectrum you posted. Are there others where > this is not the case? > > Cheers, > --Luis > > > On Thu, Sep 8, 2022 at 2:28 PM 'Eric Deutsch' via spctools-discuss < > spctools-discuss@googlegroups.com> wrote: > >> I’m thinking that ion trap spectra are usually unsuitable for TMT: >> >> >> <image001.png> >> >> >> I think you would want to acquire fragmentation spectra with Orbitrap HCD? >> >> >> >> *From:* spctools-discuss@googlegroups.com < >> spctools-discuss@googlegroups.com> *On Behalf Of *Yasir Ahmed >> *Sent:* Thursday, September 8, 2022 2:19 PM >> *To:* spctools-discuss@googlegroups.com >> *Subject:* Re: [spctools-discuss] Libra quantification on TMT 16-plex >> returns zeros only >> >> >> Hi Luis, >> >> >> Just to follow up: I found a handful of cases where one of the channels >> has super high quantification and observable reporter ions (see screenshots >> below), albeit it should be way more than this, I believe. I’ll keep >> digging, but let me know if you have any other ideas. >> >> >> Again, thanks for you suggestions. >> >> >> Cheers, >> >> Yasir >> >> >> <image002.png> >> >> >> <image003.png> >> >> >> <image004.png> >> >> >> >> On Sep 8, 2022, at 5:07 PM, Yasir Ahmed <yazah...@gmail.com> wrote: >> >> >> Hi Luis, >> >> >> Thanks a lot for the response. >> >> >> Can you try re-running Libra without the centroiding option? (i.e. set >> type="0") Or are your mzML data not centroided? >> >> >> >> I just tried that, but no difference in outcome. >> >> >> >> Another thing to try: are you able to open the PeptideProphet + Libra >> results in the PepXMLViewer? You should be able to see if there are a >> significant number of quantified PSMs -- you should also be able to examine >> a few individual spectra and zoom in on the reporter ion signals. >> >> >> >> I’m able to look at a few individual spectra, and I think they all look >> mostly good—but frankly I’m not too sure how to evaluate their suitability >> (see example screenshots below). >> >> >> >> Lastly, what version of TPP are you running? >> >> >> >> 6.1.0 >> >> >> Thanks again! >> >> Yasir >> >> >> <Screen Shot 2022-09-08 at 5.00.50 PM.png> >> >> >> <Screen Shot 2022-09-08 at 5.01.42 PM.png> >> >> >> >> >> >> >> Cheers, >> >> --Luis >> >> >> >> On Thu, Sep 8, 2022 at 12:02 PM Yasir Ahmed <yazah...@gmail.com> wrote: >> >> Greetings, >> >> >> I'm having difficulty performing TMT quantification using Libra on a >> 16-plex dataset. Basically, the "quantification.tsv" file that Libra >> outputs only contains zeros for both peptides and proteins. The Comet >> search runs just fine. I'm at a loss for where things are going wrong. The >> Mass Spec facility used ProteomeDiscoverer for the quantification, and it >> worked fine so the issue is not the raw data. >> >> >> My TPP run repository can be found here >> <https://github.com/YazBraimah/TPP_TMT_proteomics_pipeline>, and the >> "condition.xml" file for Libra—along with the Comet params file—is in the >> "params" folder. The commands used to run the TPP processes can be found in >> the file called "Snakefile". I'm happy to provide any additional >> information needed to help troubleshoot this. Any pointers/advise would be >> greatly appreciated. >> >> >> Cheers, >> >> Yasir >> >> >> -- >> 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/7cb42706-53ae-4c94-acd2-ea0293fea8b2n%40googlegroups.com >> <https://groups.google.com/d/msgid/spctools-discuss/7cb42706-53ae-4c94-acd2-ea0293fea8b2n%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/CACyS9bo%3DQxLBhn3H%2B7cg9pTKXu1Yp1bTLwb%2BfF%3DR4y%2BujoF%3DxQ%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/CACyS9bo%3DQxLBhn3H%2B7cg9pTKXu1Yp1bTLwb%2BfF%3DR4y%2BujoF%3DxQ%40mail.gmail.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/5C533052-EF37-4516-AE3D-D90A364E5E68%40gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/5C533052-EF37-4516-AE3D-D90A364E5E68%40gmail.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/aad015ab22f19ee0cea8cd2cdc24627d%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/aad015ab22f19ee0cea8cd2cdc24627d%40mail.gmail.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/CACyS9boObJ2nFUNDd_1K%2BMghDJy62GQEYu4R6zRn2CuS-7JwBQ%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CACyS9boObJ2nFUNDd_1K%2BMghDJy62GQEYu4R6zRn2CuS-7JwBQ%40mail.gmail.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/7EBE121E-E4BC-495C-B288-EE9B84CA78F9%40gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/7EBE121E-E4BC-495C-B288-EE9B84CA78F9%40gmail.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/CACyS9bqoH%2BewobE-CSZ6uQbVqAxjseAG3-_027Jk6CBkp15_Fg%40mail.gmail.com.
