Re: [spctools-discuss] TPP installation tutorials 404 errors?
Thanks Luis, your direct link works for me! Looks like clicking the hyperlinks on the tutorials page is redirecting me to URLs like the following for some reason: https://cytoscape.org/wiki/index.php?title=Linux_Installation_Guides Copying the link address from those hyperlinks sends me to the correct place though... may just be an issue on my end. Appreciate your help regardless! -Will On Friday, January 12, 2024 at 12:40:59 PM UTC-5 Luis Mendoza wrote: > Hi Will, > The following three links do work for me at the moment: > [image: image.png] > > e.g. > [image: image.png] > > I'll check with our internal IT to see if there have been any changes to > the web servers or network that may be affecting access from external users. > > In the meantime, here is the direct link, in case that helps: > > http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image > > Thanks for reporting the issue! > --Luis > > On Fri, Jan 12, 2024 at 9:34 AM Will Comstock wrote: > >> Hi all, the link to the Docker Installation Tutorial appears to be >> broken. Is there another place for me to find this tutorial? >> >> Actually, the first three links on this page all lead to 404 errors for >> me: >> http://www.tppms.org/tutorials/ >> >> Thank you! >> -Will >> >> [image: Screenshot 2024-01-12 at 12.30.17 PM.png] >> >> -- >> 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/7f9de02d-f10f-42f2-afba-821f4b296eddn%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/7f9de02d-f10f-42f2-afba-821f4b296eddn%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/979cdfb6-8b20-4e74-85fb-44f93da296c7n%40googlegroups.com.
[spctools-discuss] TPP installation tutorials 404 errors?
Hi all, the link to the Docker Installation Tutorial appears to be broken. Is there another place for me to find this tutorial? Actually, the first three links on this page all lead to 404 errors for me: http://www.tppms.org/tutorials/ Thank you! -Will [image: Screenshot 2024-01-12 at 12.30.17 PM.png] -- 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/7f9de02d-f10f-42f2-afba-821f4b296eddn%40googlegroups.com.
Re: [spctools-discuss] Optimal hardware for TPP server?
Thank you Eric, this is very good to know! We'll probably stick with something similar to our current specifications in this case. Best, -Will On Friday, October 6, 2023 at 1:35:27 AM UTC-4 Eric Deutsch wrote: > Hi Will, thanks for the question. There no easy answer. An SSD is good > because there’s a lot of disk I/O processing data. Comet itself is pretty > thrifty with memory, so you won’t need lots of memory for Comet. The > Prophets can use a lot of memory if you process huge experiments at once, > although they can often be broken up into pieces. Many of our cluster nodes > have only 96 GB of RAM and do fine for most datasets. I would probably > spend more on cores than on RAM. The machine you list there with 64 cores > and 128 GB is a good choice. If you can spend more than that, I think I > would increase the core count over more than 128 GB. A GPU won’t help for > Comet and the Prophets, so I would save money and go without the GPU. > > > > Regards, > > Eric > > > > > > > > *From:* spctools...@googlegroups.com *On > Behalf Of *Will Comstock > *Sent:* Wednesday, October 4, 2023 10:57 AM > *To:* spctools-discuss > *Subject:* [spctools-discuss] Optimal hardware for TPP server? > > > > Hi all, > > > > Kind of a naive tech question, but my lab is going to purchase a Linux > server to run the TPP and we're trying to decide on a hardware > configuration that would let us run Comet, PeptideProphet, PTM Prophet, > XPRESS, Libra, and a few other modules at robust speeds. > > > > We currently run the TPP locally on a Windows PC with 64 cores (AMD > Threadripper 3990X) and 128gb of RAM running on an SSD. Would a stronger > CPU or more RAM (or even a GPU) give us any significant boost in search > speeds if we're running a Docker image of the TPP on a Linux server? > > > > Thank you! > > -Will > > -- > 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/71df6d40-cadf-4009-8f91-78a41dae7e6bn%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/71df6d40-cadf-4009-8f91-78a41dae7e6bn%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/94852e3e-a0bd-4e83-8bd4-54009c2600e9n%40googlegroups.com.
[spctools-discuss] Optimal hardware for TPP server?
Hi all, Kind of a naive tech question, but my lab is going to purchase a Linux server to run the TPP and we're trying to decide on a hardware configuration that would let us run Comet, PeptideProphet, PTM Prophet, XPRESS, Libra, and a few other modules at robust speeds. We currently run the TPP locally on a Windows PC with 64 cores (AMD Threadripper 3990X) and 128gb of RAM running on an SSD. Would a stronger CPU or more RAM (or even a GPU) give us any significant boost in search speeds if we're running a Docker image of the TPP on a Linux server? Thank you! -Will -- 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/71df6d40-cadf-4009-8f91-78a41dae7e6bn%40googlegroups.com.
Re: [spctools-discuss] SILAC quantification with targeted SIM
Okay I got it to work. For the record, my solution was the following: 1. Rather than use the msConvert packaged with the TPP, I downloaded it separately from ProteoWizard. 2. I converted my RAW file with the following parameters: - [image: SIM_msConvert.PNG] - (I am not sure if "SRM as spectra" is required, but "SIM as spectra" was key as all my MS1 scans were classified as SIM-MS scans) 3. I then searched the resulting mzML file as normal. Thanks again, Jimmy! -Will On Friday, April 7, 2023 at 1:04:44 PM UTC-4 Will Comstock wrote: > Good catch, I will try to redo the RAW conversion to include my MS1 scans. > Thanks Jimmy! > > -Will > > On Fri, Apr 7, 2023 at 12:50 PM Jimmy Eng wrote: > >> Will, >> >> XPRESS extracts precursor intensities from MS1 scans and your mzXML file >> contains only MS/MS scans. So that's why XPRESS is failing because it's >> expecting to parse MS1 scans which aren't present in this file. >> >> Jimmy >> >> On Fri, Apr 7, 2023 at 8:57 AM Will Comstock wrote: >> >>> Hi all, >>> >>> I'm trying to use tSIM-ddMS2 to identify specific peptides in my sample, >>> but I also want SILAC quantification of those peptides using XPRESS. I've >>> made sure the MS1 isolation window is wide enough to see both Light and >>> Heavy peptide peaks for everything in my inclusion list (30 daltons, so my >>> heavy peptides which are +8 or +10 are detected). However, when I search >>> with Comet and XPRESS, there is no quantitative ratio provided, just -1.0. >>> XPRESS appears to be looking in the wrong place for the light and heavy >>> peptides, but I am not sure why or how to redirect it to the right parts of >>> my MS1 spectra. If I look at the precursor scans manually via QualBrowser, >>> both peaks are definitely being detected. >>> >>> Has anyone here tried using XPRESS to do SILAC quantitation in targeted >>> runs before? >>> >>> >>> Here is a folder with my data, search parameters, and database just in >>> case. >>> >>> https://drive.google.com/drive/folders/1142YHaxB1RC6HMcfuy_MdEN8T-sSLDSl?usp=sharing >>> >>> Thanks! >>> -Will >>> >>> -- >>> 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/445ec267-3132-40ca-89c7-9d62b7c0a993n%40googlegroups.com >>> >>> <https://groups.google.com/d/msgid/spctools-discuss/445ec267-3132-40ca-89c7-9d62b7c0a993n%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- >> > You received this message because you are subscribed to a topic in the >> Google Groups "spctools-discuss" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/spctools-discuss/6-Q5KuqumMQ/unsubscribe >> . >> To unsubscribe from this group and all its topics, send an email to >> spctools-discu...@googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EOFuHubneYYdcL0Z1cUqiJRi%3Ds%2B%2BrmjXgz9otBT5zDMtg%40mail.gmail.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EOFuHubneYYdcL0Z1cUqiJRi%3Ds%2B%2BrmjXgz9otBT5zDMtg%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/f5a47108-95f1-4f8b-a44b-ca48a6c6cdafn%40googlegroups.com.
Re: [spctools-discuss] SILAC quantification with targeted SIM
Good catch, I will try to redo the RAW conversion to include my MS1 scans. Thanks Jimmy! -Will On Fri, Apr 7, 2023 at 12:50 PM Jimmy Eng wrote: > Will, > > XPRESS extracts precursor intensities from MS1 scans and your mzXML file > contains only MS/MS scans. So that's why XPRESS is failing because it's > expecting to parse MS1 scans which aren't present in this file. > > Jimmy > > On Fri, Apr 7, 2023 at 8:57 AM Will Comstock wrote: > >> Hi all, >> >> I'm trying to use tSIM-ddMS2 to identify specific peptides in my sample, >> but I also want SILAC quantification of those peptides using XPRESS. I've >> made sure the MS1 isolation window is wide enough to see both Light and >> Heavy peptide peaks for everything in my inclusion list (30 daltons, so my >> heavy peptides which are +8 or +10 are detected). However, when I search >> with Comet and XPRESS, there is no quantitative ratio provided, just -1.0. >> XPRESS appears to be looking in the wrong place for the light and heavy >> peptides, but I am not sure why or how to redirect it to the right parts of >> my MS1 spectra. If I look at the precursor scans manually via QualBrowser, >> both peaks are definitely being detected. >> >> Has anyone here tried using XPRESS to do SILAC quantitation in targeted >> runs before? >> >> >> Here is a folder with my data, search parameters, and database just in >> case. >> >> https://drive.google.com/drive/folders/1142YHaxB1RC6HMcfuy_MdEN8T-sSLDSl?usp=sharing >> >> Thanks! >> -Will >> >> -- >> 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/445ec267-3132-40ca-89c7-9d62b7c0a993n%40googlegroups.com >> <https://groups.google.com/d/msgid/spctools-discuss/445ec267-3132-40ca-89c7-9d62b7c0a993n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/6-Q5KuqumMQ/unsubscribe > . > To unsubscribe from this group and all its topics, 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/CAJqD6EOFuHubneYYdcL0Z1cUqiJRi%3Ds%2B%2BrmjXgz9otBT5zDMtg%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EOFuHubneYYdcL0Z1cUqiJRi%3Ds%2B%2BrmjXgz9otBT5zDMtg%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/CALJ7d9ytOk%2BPCPZU2Qw3PLZ_qq3b2QqtwBkYs3unMS96SMtFgQ%40mail.gmail.com.
[spctools-discuss] SILAC quantification with targeted SIM
Hi all, I'm trying to use tSIM-ddMS2 to identify specific peptides in my sample, but I also want SILAC quantification of those peptides using XPRESS. I've made sure the MS1 isolation window is wide enough to see both Light and Heavy peptide peaks for everything in my inclusion list (30 daltons, so my heavy peptides which are +8 or +10 are detected). However, when I search with Comet and XPRESS, there is no quantitative ratio provided, just -1.0. XPRESS appears to be looking in the wrong place for the light and heavy peptides, but I am not sure why or how to redirect it to the right parts of my MS1 spectra. If I look at the precursor scans manually via QualBrowser, both peaks are definitely being detected. Has anyone here tried using XPRESS to do SILAC quantitation in targeted runs before? Here is a folder with my data, search parameters, and database just in case. https://drive.google.com/drive/folders/1142YHaxB1RC6HMcfuy_MdEN8T-sSLDSl?usp=sharing Thanks! -Will -- 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/445ec267-3132-40ca-89c7-9d62b7c0a993n%40googlegroups.com.
[spctools-discuss] Windows 11 Compatibility
Hi all, Very quick question: Is the TPP 6.1.0 fully compatible with Windows 11? Thanks! -Will -- 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/4ec72f60-e76b-4f22-af53-047d08d9db4fn%40googlegroups.com.
Re: [spctools-discuss] Install without reboot?
Hi Eric, Your advice worked! For the record, I did the following: 1. Installed the TPP v6.1 on the PCs running Windows 10 2. Entered directory C:/TPP/bin 3. Ran "tpptray.bat" 4. Clicked the TPP in the Windows tray and clicked "Start TPP web server" 5. Opened Petunia successfully I appreciate your prompt help with this, -Will On Thursday, September 8, 2022 at 2:32:17 PM UTC-4 Eric Deutsch wrote: > Hi Will, I think the answer is yes, although I’d need to test on a fresh > computer for the exact protocol. I think you can launch the TPP Tray app > and then use that to start Apache and then you’re good to go. Is this for > Windows computers? > > > > Eric > > > > > > *From:* spctools...@googlegroups.com *On > Behalf Of *Will Comstock > *Sent:* Thursday, September 8, 2022 7:44 AM > *To:* spctools-discuss > *Subject:* [spctools-discuss] Install without reboot? > > > > I'm teaching a small mass spec course and I have a TPP demonstration > planned for the students, but unfortunately the institute computers wipe > upon restart. Is there any way for the students to install the TPP and > access the Petunia interface without having to reboot the computers? Can > the TPP be installed on and run from a USB drive instead of the computer > itself? > > > > Thanks, > > -Will Comstock > > > > > > -- > 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/6dc44bb8-a0f7-4be1-95a5-4a2c4d7db429n%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/6dc44bb8-a0f7-4be1-95a5-4a2c4d7db429n%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/d3197f05-d2f9-4d45-9a64-62fa5fcee185n%40googlegroups.com.
[spctools-discuss] Install without reboot?
I'm teaching a small mass spec course and I have a TPP demonstration planned for the students, but unfortunately the institute computers wipe upon restart. Is there any way for the students to install the TPP and access the Petunia interface without having to reboot the computers? Can the TPP be installed on and run from a USB drive instead of the computer itself? Thanks, -Will Comstock -- 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/6dc44bb8-a0f7-4be1-95a5-4a2c4d7db429n%40googlegroups.com.
[spctools-discuss] Re: TPP Comet search time-out
I have also been encountering this issue and would love to hear a solution. The search still reads as "Running" but simply stops searching any more mzML files. Depending on the size of my files, the search times out at different points, but will almost never search more than 8 files at a time. Happy to provide an example dataset + parameters + FASTA file if anyone wants to try and replicate the timeout. -Will On Wednesday, November 10, 2021 at 1:32:09 AM UTC-5 steven...@gmail.com wrote: > Hi everyone, > > I've been using TPP for a little while now for the analysis of my data. I > have been using Comet to perform database searching on a large number of > mzml files and have noticed that the analysis will usually time out after > about 6 hours. In this case, I will remove the mzml files that have been > successfully processed and then re-run comet. Is this job time-out an > inherent part of TPP, or is it a setting that can be changed? If the > latter, are there any risks in running the analysis for over 6 hours? > > Thanks in advance for any advice > Steven > -- 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/d7d9a7b5-fe88-40c3-89b6-b23009a13d2fn%40googlegroups.com.
Re: [spctools-discuss] Precursor Intensity after Comet search
Thank you David, exactly what I was looking for! Best, -Will On Thursday, September 16, 2021 at 11:31:43 AM UTC-4 David Shteynberg wrote: > Hi Will, > > You can use option -PREC in advanced options for xinteract "Analyze > Peptides" results to populate this column.Alternatively you can run > InteractParser with -I flag to get the same values in the pepXML results. > > Cheers, > -David > > On Thu, Sep 16, 2021 at 8:11 AM Will Comstock wrote: > >> Hello, >> >> After Comet searching mzXML files, appending the "Precursor Intensity" >> column in the pepXML viewer reveals that it contains no values. Is there a >> way to make Comet retrieve/retain precursor intensities for later use? >> Would running XPRESS in label-free mode essentially accomplish this? I am >> using TPP 6.0 for these analyses. >> >> Respectfully, >> -Will Comstock >> >> -- >> 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/862b0547-7498-46db-b660-2ee6e53c42f4n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/862b0547-7498-46db-b660-2ee6e53c42f4n%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/012df94b-cc15-49c7-b05a-5c18f231e0f1n%40googlegroups.com.
[spctools-discuss] Precursor Intensity after Comet search
Hello, After Comet searching mzXML files, appending the "Precursor Intensity" column in the pepXML viewer reveals that it contains no values. Is there a way to make Comet retrieve/retain precursor intensities for later use? Would running XPRESS in label-free mode essentially accomplish this? I am using TPP 6.0 for these analyses. Respectfully, -Will Comstock -- 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/862b0547-7498-46db-b660-2ee6e53c42f4n%40googlegroups.com.
Re: [spctools-discuss] TPP 6.0 Libra Error
Hi David, It works! Thanks very much for addressing this issue so promptly. Best, -Will On Friday, September 3, 2021 at 9:24:36 PM UTC-4 David Shteynberg wrote: > Hi Will, > > I was able to trace this to a memory issue in the code and correct it. I > have posted a patched version here: > > > https://drive.google.com/file/d/1jiGuyLDC1E504GvnG_MqX7R6J4NWe_2D/view?usp=sharing > > > Replace your copy in C:\TPP\bin or where you installed your TPP. > > > Please let me know if you have any questions or issues with the new > executable. > > Thanks, > -David > > On Fri, Sep 3, 2021 at 9:34 AM Will Comstock wrote: > >> Hi David, >> >> Here is a Google Drive folder containing all the files used in the >> search. A .txt file with the error message I encountered is included, as >> well as a screenshot of the Peptide Prophet parameters I used. >> >> >> https://drive.google.com/drive/folders/1xS8GdvOFw7tVMNLzObC_3tz1cttX_kLw?usp=sharing >> >> I appreciate the help! >> -Will >> >> On Friday, September 3, 2021 at 12:21:13 PM UTC-4 David Shteynberg wrote: >> >>> Hello William, >>> >>> Sorry to hear you are having trouble with Libra. If you are able to >>> post the data for me to reproduce the problem I will attempt to patch it up. >>> >>> Thank you! >>> >>> -David >>> >>> >>> >>> On Fri, Sep 3, 2021 at 8:02 AM Will Comstock wrote: >>> >>>> Hello, >>>> >>>> Our lab just updated from 5.2 to 6.0 and is testing some datasets that >>>> were formerly searched with 5.2. >>>> >>>> We are now consistently encountering an error when running Libra after >>>> PeptideProphet, preventing the reporter ion quantitation from completing. >>>> The resulting interact.pep.xml is still able to be opened, there is just >>>> no >>>> Libra result appended to the table. >>>> >>>> Here is the Libra error encountered: >>>> [image: TPP6_LibraError.PNG] >>>> >>>> The return code is 29696. What could be causing this, and how might we >>>> try fixing it? >>>> >>>> Thank you, >>>> -Will Comstock >>>> >>>> -- >>>> 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/6ced026c-485f-4b4e-8ef1-02fe487234a0n%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/spctools-discuss/6ced026c-485f-4b4e-8ef1-02fe487234a0n%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/107618af-5a58-4508-84eb-23a6598121a9n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/107618af-5a58-4508-84eb-23a6598121a9n%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/9d31769a-e7a1-469d-ace1-7428a0c97ef3n%40googlegroups.com.
Re: [spctools-discuss] TPP 6.0 Libra Error
Hi David, Here is a Google Drive folder containing all the files used in the search. A .txt file with the error message I encountered is included, as well as a screenshot of the Peptide Prophet parameters I used. https://drive.google.com/drive/folders/1xS8GdvOFw7tVMNLzObC_3tz1cttX_kLw?usp=sharing I appreciate the help! -Will On Friday, September 3, 2021 at 12:21:13 PM UTC-4 David Shteynberg wrote: > Hello William, > > Sorry to hear you are having trouble with Libra. If you are able to post > the data for me to reproduce the problem I will attempt to patch it up. > > Thank you! > > -David > > > > On Fri, Sep 3, 2021 at 8:02 AM Will Comstock wrote: > >> Hello, >> >> Our lab just updated from 5.2 to 6.0 and is testing some datasets that >> were formerly searched with 5.2. >> >> We are now consistently encountering an error when running Libra after >> PeptideProphet, preventing the reporter ion quantitation from completing. >> The resulting interact.pep.xml is still able to be opened, there is just no >> Libra result appended to the table. >> >> Here is the Libra error encountered: >> [image: TPP6_LibraError.PNG] >> >> The return code is 29696. What could be causing this, and how might we >> try fixing it? >> >> Thank you, >> -Will Comstock >> >> -- >> 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/6ced026c-485f-4b4e-8ef1-02fe487234a0n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/6ced026c-485f-4b4e-8ef1-02fe487234a0n%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/107618af-5a58-4508-84eb-23a6598121a9n%40googlegroups.com.
[spctools-discuss] TPP 6.0 Libra Error
Hello, Our lab just updated from 5.2 to 6.0 and is testing some datasets that were formerly searched with 5.2. We are now consistently encountering an error when running Libra after PeptideProphet, preventing the reporter ion quantitation from completing. The resulting interact.pep.xml is still able to be opened, there is just no Libra result appended to the table. Here is the Libra error encountered: [image: TPP6_LibraError.PNG] The return code is 29696. What could be causing this, and how might we try fixing it? Thank you, -Will Comstock -- 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/6ced026c-485f-4b4e-8ef1-02fe487234a0n%40googlegroups.com.
Re: [spctools-discuss] PTMProphet command failure (for larger datasets?)
Hi David, An update just in case anyone else has run into our issue: I copied the PTMProphetParser.exe from a 6.0.0 installation over into our current 5.2.0 installation, and everything is working great thus far! Thank you for the tip, I appreciate the assistance. Respectfully, -Will On Tuesday, March 16, 2021 at 8:46:35 PM UTC-4 David Shteynberg wrote: > Hi Will, > > There is a release candidate for version 6.0.0 available on sourceforge: > > https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v6.0%20%28Release%20Candidates%29/ > > If you do end up trying it let me know if you find any issues. > > Thanks! > -David > > On Tue, Mar 16, 2021 at 5:14 PM Will Comstock wrote: > >> Hi David, >> >> I'll attempt to re-run PTMProphet analysis on a few problematic datasets >> with MAXTHREADS=1. >> >> I am currently using the version of PTMProphet that came with the >> installation of TPP 5.2. Is there a newer version available that I could be >> using instead? >> >> Thanks for your help! >> -Will >> >> On Tuesday, March 16, 2021 at 7:37:58 PM UTC-4 David Shteynberg wrote: >> >>> Hello Will, >>> >>> We routinely run PTMProphet on datasets containing multiple hundreds of >>> thousands of PSMs. This looks like multithreading issue >>> related MAXTHREADS=0 parameter, this should not happen if you use >>> MAXTHREADS=1. I have corrected several bugs related to multithreading in >>> the codebase. Which version of PTMProphet are you using? >>> >>> Thanks, >>> -David >>> >>> On Tue, Mar 16, 2021 at 3:59 PM Will Comstock wrote: >>> >>>> Hey everyone, >>>> >>>> I've run into an issue with PTMProphet where occasionally the command >>>> will fail for unknown reasons and the resulting ptm.pep.xml cannot be >>>> opened with the PepXML viewer. The command log seems to cut off abruptly, >>>> as pictured in the attached screenshot. Also attached is the page that >>>> appears upon trying to open the ptm.pep.xml. >>>> >>>> The interact.pep.xml files we're analyzing clock in at about 200 to 250 >>>> megabytes. As a workaround, we currently just split the initial batch of >>>> pep.xmls into smaller groups before running PeptideProphet and PTMProphet >>>> on them again. Sometimes we end up with batches of pep.xmls as small as 3 >>>> or 4 files, which is somewhat inconvenient for projects with hundreds of >>>> RAW files. >>>> >>>> Is there another way around this issue? We've tried running it through >>>> the command line as well and this problem still crops up frequently. >>>> [image: PTMproph_CommandFailed.png] >>>> [image: PTMproph_CommandFailed_xmlError.png] >>>> Thanks! >>>> >>>> -- >>>> 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/020c5be3-14ad-4350-9b12-dbb366fdb2c8n%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/spctools-discuss/020c5be3-14ad-4350-9b12-dbb366fdb2c8n%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/22052f7c-d0d9-494e-8208-b49b29fb8321n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/22052f7c-d0d9-494e-8208-b49b29fb8321n%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/b5eceb74-1e34-4c71-9f09-27b1e266ec89n%40googlegroups.com.
Re: [spctools-discuss] PTMProphet command failure (for larger datasets?)
Hi David, I'll attempt to re-run PTMProphet analysis on a few problematic datasets with MAXTHREADS=1. I am currently using the version of PTMProphet that came with the installation of TPP 5.2. Is there a newer version available that I could be using instead? Thanks for your help! -Will On Tuesday, March 16, 2021 at 7:37:58 PM UTC-4 David Shteynberg wrote: > Hello Will, > > We routinely run PTMProphet on datasets containing multiple hundreds of > thousands of PSMs. This looks like multithreading issue > related MAXTHREADS=0 parameter, this should not happen if you use > MAXTHREADS=1. I have corrected several bugs related to multithreading in > the codebase. Which version of PTMProphet are you using? > > Thanks, > -David > > On Tue, Mar 16, 2021 at 3:59 PM Will Comstock wrote: > >> Hey everyone, >> >> I've run into an issue with PTMProphet where occasionally the command >> will fail for unknown reasons and the resulting ptm.pep.xml cannot be >> opened with the PepXML viewer. The command log seems to cut off abruptly, >> as pictured in the attached screenshot. Also attached is the page that >> appears upon trying to open the ptm.pep.xml. >> >> The interact.pep.xml files we're analyzing clock in at about 200 to 250 >> megabytes. As a workaround, we currently just split the initial batch of >> pep.xmls into smaller groups before running PeptideProphet and PTMProphet >> on them again. Sometimes we end up with batches of pep.xmls as small as 3 >> or 4 files, which is somewhat inconvenient for projects with hundreds of >> RAW files. >> >> Is there another way around this issue? We've tried running it through >> the command line as well and this problem still crops up frequently. >> [image: PTMproph_CommandFailed.png] >> [image: PTMproph_CommandFailed_xmlError.png] >> Thanks! >> >> -- >> 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/020c5be3-14ad-4350-9b12-dbb366fdb2c8n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/020c5be3-14ad-4350-9b12-dbb366fdb2c8n%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/22052f7c-d0d9-494e-8208-b49b29fb8321n%40googlegroups.com.
