Re: [spctools-discuss] PepXML Schema v1.23

Hello Max, Thank you for bringing this to our attention. I have added the file and updated the wiki. Cheers, --Luis On Sat, Feb 17, 2024 at 9:20 AM Max Brazhnikov wrote: > Hi all, > > pepXML_v123.xsd was committed almost two years ago [1], however pepXML > wiki page [2] has ceased at v1.22,

Re: [spctools-discuss] PepXML > spectrum > top hits viewer issue - Comet

Hi Sam, It does sound like potentially an issue with the mzML file path(s) inside the comet pepXML results, though there could be other issues. As for troubleshooting, you can inspect the URL of those troublesome links and look for the Dta= (or File=) parameter -- is the filepath the same that

Re: [spctools-discuss] Trouble converting Waters.RAW with TPP msconvert

Hello Alex, Glad that you were able to get to the bottom of this issue and hope you have been able to process your data. I just wanted to add that when installing TPP on Windows, the entire ProteoWizard set of tools (including msConvert GUI) is also bundled -- so there is typically no need to

Re: [spctools-discuss] TPP installation tutorials 404 errors?

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. >> [

Re: [spctools-discuss] Problem with PeptideProphet

Hello Tanmay, How did you generate the input pepXML files? Which search engine did you use? Are you able to open both of those files and verify that they have results? Can you process results from another search engine (e.g. Comet or X!Tandem) of the same mzML data? Cheers, --Luis On Wed, Jul

Re: [spctools-discuss] converting prot.xml to tsv/something else

Hi Emma, The ProtXMLViewer is under the cgi-bin/ directory of the image. However, the version in 6.2.0 does not have the command-line capability of exporting protXML to TSV. We introduced this feature in 6.3.0, and will be available once we produce the related image. (well, after fixing some

Re: [spctools-discuss] Variable mod query in COMET

oup as well. They will > probably come up with an update or something to enable it. > On Tuesday, August 1, 2023 at 8:47:46 AM UTC+5:30 Luis Mendoza wrote: > >> Hi Debojyoti, >> Yes, I would say this is the most straightforward way of conducting this >> search. >> No

Re: [spctools-discuss] Variable mod query in COMET

Hi Debojyoti, Yes, I would say this is the most straightforward way of conducting this search. Note that you may need to make further adjustments to the variable mod string settings if, say, a given peptide must have *all* of its Cysteines in one state (+50) or the other (+90). The default is to

Re: [spctools-discuss] Access to Mascot file results

Hello Carlo, I recall seeing a report like this years ago, and I think it has to do with configuring the Mascot server to open its port. I forget the details of how this is done, and we don't have a Mascot server in-house where we can test; perhaps someone else is able to provide help on this.

Re: [spctools-discuss] Re: Upcoming Trans-Proteomic Pipeline (TPP) course

ear Luis, > > Please send the link of the registration form. > > Regards > > On Fri, Jul 21, 2023 at 1:42 PM 'Luis Mendoza' via spctools-discuss < > spctools-discuss@googlegroups.com> wrote: > >> Hello Emma, Manuela, and others interested in attending virtually, &g

Re: [spctools-discuss] Re: Upcoming Trans-Proteomic Pipeline (TPP) course

ng this. Will there be an option to attend virtually? >> I am not based in the US so would find it impossible to attend on short >> notice. >> >> All the best, >> Emma >> >> On Thursday, 20 July 2023 at 01:50:49 UTC+2 Luis Mendoza wrote: >>

Re: [spctools-discuss] Re: Next proteomics informatics course?

ity rules) on such > short notice. > Thanks, > Don > > On Tue, Jul 18, 2023 at 3:44 PM 'Luis Mendoza' via spctools-discuss < > spctools-discuss@googlegroups.com> wrote: > >> Hello all, >> Based on the survey of dates that Eric sent out, we will hold a short TPP >> c

Re: [spctools-discuss] Re: Next proteomics informatics course?

Hello all, Based on the survey of dates that Eric sent out, we will hold a short TPP course next week, July 26 - 28, at ISB. We will send a link to registration and more info in the next couple of days, but expect to go 8am - 4:30pm on those three days. Hope this date works for most of you! --Luis

Re: [spctools-discuss] TPP Tandem input files

Hello Emma, According to this, X!Tandem is indeed able to process MGF files: https://www.thegpm.org/tandem/tandem_install_faq.html#faq6 Do note that the TPP GUI (Petunia) only allows you to choose mzML/mzXML files as input, so you will have to run via the command-line. Also, any downstream TPP

[spctools-discuss] TPP @ ASMS 2023 -- Posters, Tuesday Workshop, and Bioinformatics Hub

nd Out with PeptidePrisoner!* Luis Mendoza *MP 376 * - *Ving: A New Tool in the Trans-Proteomic Pipeline for XL-MS Using Cleavable Cross-Linking Reagents* Michael Hoopmann *TP 174 * - * Modification Specific Modeling in PeptideProphet Improves Validation of Rare PTM Containing Pe

[spctools-discuss] TPP 6.3.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.3.0 "Arcus" We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 6.3.0. The software is available for Windows as well as Linux from all the usual locations (please see the section below,

Re: [spctools-discuss] protein validation

Hello Felipe, There may be several reasons why you see the viral protein in your analysis, e.g. - Did you only run Comet, or did you validate using the TPP/Prophets? If the latter, what was the probability of the protein(s) in question? - What were the contents of the database that you

Re: [spctools-discuss] Problem with PTMprophet

gt; > Felipe > > El vie, 28 abr 2023 a las 4:58, 'Luis Mendoza' via spctools-discuss (< > spctools-discuss@googlegroups.com>) escribió: > >> Hello Felipe, >> >> It is in general not normal to not find "any results" with TPP when other >>

Re: [spctools-discuss] Problem with PTMprophet

Hello Felipe, It is in general not normal to not find "any results" with TPP when other platforms do find some, as there is often partial, if not significant, overlap. Typically when no results are found, it points to either bad data (presumably not in this case) or incorrect parameters

Re: [spctools-discuss] SILAC quantification with targeted SIM

Hi Will, Glad you got this to work! A potentially quicker solution is to enter those extra flags in the "additional options" box in Petunia: [image: image.png] You can find a full set of available options at the Proteowizard msconvert info page:

Re: [spctools-discuss] Re: Output sequence coverage info

s! --Luis On Tue, Mar 28, 2023 at 3:59 PM Yasir Ahmed wrote: > Thanks Luis, that's helpful. For now I'll just use an older version of TPP > to get the coverage values. > > Cheers, > Yasir > > On Tuesday, March 28, 2023 at 6:46:58 PM UTC-4 Luis Mendoza wrote: > >&

Re: [spctools-discuss] Re: Output sequence coverage info

Hello Yasir, We have recently identified a bug in ProteinProphet that mis-reports the coverage as zero for all proteins. This affects TPP versions 6.1.0 and 6.2.0. We will be releasing an update soon that corrects this and other bugs. Even then, the value that is reported in protXML is the

[spctools-discuss] TPP 6.2.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.2.0 "Nacreous" We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 6.2.0. The software is available for Windows as well as Linux from all the usual locations (please see the section

Re: [spctools-discuss] Analyzing Metaproteomic Data

Hello, The version of msconvert that is shipped with TPP is a couple of years old and does not know about that instrument. You have three options to convert your files: 1. Download and install a newer version of ProteoWizard, run the conversion, and use that mzML file in Comet. This is likely

Re: [spctools-discuss] protein prophet failing on Eclipse searches

Hi, Congrats on the new instrument, and happy holidays as well! The error seems to indicate that there is no input data for ProteinProphet to work with; can you verify that the input file contains validated search results with probabilities above 0.2 ? Are there any other errors or warnings in

Re: [spctools-discuss] Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi

Hello, That is quite odd; Are you able to share a pepXML file so we can troubleshoot? You can contact me directly to arrange a file transfer. Thanks, --Luis On Tue, Oct 18, 2022 at 12:21 PM 2kl...@gmail.com <2kl...@gmail.com> wrote: > Hi all, > > I am using the TPP v6.1.0 Parhelion, Build

Re: [spctools-discuss] Windows 11 Compatibility

Hi Will, We tested it on Windows 11 a few months ago and noticed no issues. Please do let us know if you run into any. Cheers, --Luis On Thu, Oct 13, 2022 at 12:24 PM Will Comstock wrote: > Hi all, > > Very quick question: Is the TPP 6.1.0 fully compatible with Windows 11? > > Thanks! > -Will

Re: [spctools-discuss] Libra quantification on TMT 16-plex returns zeros only

rgetMS 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 report

Re: [spctools-discuss] Libra quantification on TMT 16-plex returns zeros only

Hello Yasir, Can you try re-running Libra without the centroiding option? (i.e. set type="0") Or are your mzML data not centroided? 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

Re: [spctools-discuss] Tandem Analysis

Hello Priti, You can specify non-enzymatic cleavage by setting the *protein, cleavage site* parameter to *[X]|[X]* . More info at the X!Tandem site: https://www.thegpm.org/TANDEM/api/pcs.html https://www.thegpm.org/TANDEM/api/pcsemi.html Hope this helps, --Luis On Wed, Aug 3, 2022 at 10:59 PM

Re: [spctools-discuss] Comet Params file for MS2 and MS3 TMT11-plex, comet won't load any spectra when mslevel=3

Hello, It seems that your issue may be caused by this parameter: ms_level = 2-3 # MS level to analyze, valid are levels 2 (default) or 3 Please specify it as a single value, e.g. ms_level = *3* # MS level to analyze, valid are levels 2 (default)

Re: [spctools-discuss] account management

Hi Malcolm, Yes, those instructions for adding new accounts are still valid; I find it simplest to follow the ones under your second link ("TPP Login Credentials"). Please do note that those passwords are only as secure as the server protocol under which you install TPP -- i.e. things are not at

Re: [spctools-discuss] Re: TPP 5.2.0 installation error CentOS 7.8

Very nice, thank you! On Fri, Jun 10, 2022 at 4:18 PM Malcolm Cook wrote: > I just finished successful install on CentOS7 with the following notes: > > https://github.com/malcook/tpp_sandbox/blob/main/tpp_install_centos7.org > > I hope it might help someone else > > On Monday, October 12,

Re: [spctools-discuss] Re: TPP 6.1.0 Release is now available

Hi Malcolm, Thank you for the congrats, and for catching that in our build notes; we will correct it soon. In the "Pulling from Sourceforge" section, just follow the commented-out command instead of the last one: #svn checkout http://svn.code.sf.net/p/sashimi/code/tags/release_6.1.0 <-

[spctools-discuss] TPP @ ASMS 2022 -- Posters and Monday Workshop

Hello everyone, The SPC software tools team will be leading an evening *Workshop on Monday June 6th at 5:45pm in room M100 BC *during the ASMS Annual Conference. We will give a brief intro to the existing TPP tools, including new features in *TPP 6.1.0*, and then encourage discussion about them

[spctools-discuss] TPP 6.1.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.1.0 "Parhelion" We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 6.1.0. The software is available for Windows as well as Linux from all the usual locations (please see the section

Re: [spctools-discuss] MzXML2Search does not create files

Hello Max, There seems to be an issue with running this command via the UI (Petunia). Can you check if you get the same behavior when running on the command-line? Thanks for reporting this. --Luis On Wed, Mar 2, 2022 at 3:56 PM Maxence Le Vasseur < levasseurmaxe...@gmail.com> wrote: > Hi there,

Re: [spctools-discuss] MzXML2Search does not create files

On Wed, Mar 2, 2022 at 3:56 PM Maxence Le Vasseur < levasseurmaxe...@gmail.com> wrote: > Hi there, > > It seems that the MzXML2Search function does not create .dta (and possibly > other) files. Running the function from the Petunia web interface creates > the folder but the folder is empty after

Re: [spctools-discuss] TPP offline version?

Hello Jill, Yes, the TPP tools are run on your computer and no internet connection is required other than to download it. Or you can install from a flash drive or other similar media as well. The only time you might need internet is to follow certain links to extra information from the various

Re: [spctools-discuss] Cannot execute 'tpp_models.pl' by 'ProphetModels.pl' in TPP_5.2.0

Hello, Is /usr/local/tpp/bin/ in your PATH? If not, please add it and try again. You can test by typing which tpp_models.pl We would also recommend installing the latest version of TPP (6.0.0), which we recently released. Hope this helps, --Luis On Mon, Aug 23, 2021 at 9:53 AM Huang

[spctools-discuss] TPP 6.0.0 Release is now available

*Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.0.0 "OmegaBlock".* We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 6.0.0. The software is available for Windows as well as Linux from all the usual locations (please see the section

Re: [spctools-discuss] Re: Exporting StPeter´s ng to mzid

Hello Valdemir, You can run the ProtXMLViewer on the command-line to do this. If you want one protein per line, with peptides as a comma-separated list: /FULL/PATH/TO/tpp/cgi-bin/ProtXMLViewer.pl -file -action ExportExcel If you want one peptide per line, with per-peptide stats as well:

Re: [spctools-discuss] TPP working directory - how to change

Hello Laco, The simplest way is to select the location of the data at the time you install TPP. If you already installed TPP, you can just run the installer again, making sure to specify the location of the data directory. (You can leave the actual TPP installation in C:\TPP if you'd like).

Re: [spctools-discuss] Error generation while converting raw files

Hello Giangiacomo, You can use the Lib2html tool to convert an splib into a webpage with clickable links to library spectra. You can launch this tool from SpectraST Tools -> Convert Libraries to HTML. Hope this helps, --Luis On Thu, Jan 21, 2021 at 12:09 AM giangiacomo beretta <

Re: [spctools-discuss] Is there a threshold of min. peptide probability that ProteinProphet uses to pick the peptides?

Hello James, Yes, these values are still hard-coded. If you wish to test alternative values, you can edit lines 958-959 and recompile: https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/src/Validation/ProteinProphet/ProteinProphet.cpp MIN_WT = 0.5; MIN_PROB =

Re: [spctools-discuss] Related to St Peter tool in TPP

Hello Mehar, It seems that there was an issue with reading your user session cookie -- perhaps you followed an old link, reinstalled TPP while logged in, or your browser does not support cookies. I suggest starting a new browser session and try to run TPP again; let us know if the issue persists.

Re: [spctools-discuss] TPP seems never stop in windows......

Hello, This is likely an issue with the webserver not realizing that X!Tandem has finished running. Can you see if there are any "tandem.exe" processes running by opening the Task Manager? - If you do not see any and if you can see .tandem output files, it means that the job is done, but the

Re: [spctools-discuss] Not all the proteins in PeptideProphet appear in ProteinProphet

Hello Soroush, Great! Good to verify that it is working as designed. And you will not miss those zero probability proteins; they would just add even more time to the processing and make a larger output file, but with no gain in high quality results. Cheers, --Luis On Tue, Nov 17, 2020 at

Re: [spctools-discuss] Not all the proteins in PeptideProphet appear in ProteinProphet

Hello Soroush, ProteinProphet has baked-in defaults in the code that will skip over any peptide with (initial) probability < 0.05 (and won't use those below 0.20 post-NSP adjustment). Do any of those peptides that point to the missing proteins violate that rule? This is certainly something that

Re: [spctools-discuss] Re: Initiating Petunia GUI after TPP installation Windows Server 2019

Hi Miguel, Glad that you were able to solve this, and sorry we could not help, as we do not have access to a WS2019 machine. Thanks for the update, and hope TPP keeps being useful to your research! --Luis On Mon, Nov 9, 2020 at 4:17 PM Miguel Cosenza wrote: > Hello, > > I managed to solve

Re: [spctools-discuss] Linux Build Error

Hi Nathan, In case you want to build something that closely resembles 5.2.0, you can follow the steps on this page: http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS making sure to use revision 7909. Alternatively, you can use an older compiler to

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

Hello Emily, This is not a problem that we have seen much of. Do you know which version of ProteinProphet / TPP you are using? One potential issue is the large number of proteins (and peptides) that it is trying to process -- can you either monitor the memory usage of the machine when you run

Re: [spctools-discuss] LFQ

The other alternative is to run XPRESS in Label-free mode. For peaks where it can extract intensities, it will report two results: one for the integrated area with corresponding scan range, and one for the maximum peak intensity along with the scan number of that peak. You can view and export

Re: [spctools-discuss] ProtyQuant for comparing TPP samples (.pepXML)

This looks great! Thank you. Robert! --Luis On Fri, Sep 25, 2020 at 1:34 PM Robert wrote: > Hi, I just published a software for post-processing TPP .pepXML files > (validated by PeptideProphet). The GUI software has the following functions: > > - Calculation of protein inference/

Re: [spctools-discuss] Query related to PTMprophet results in TPP

Hello Mehar, Unfortunately PTMProphet does not calculate the protein position of the modified amino acids; we may add this to a future version of TPP. In the meantime, you would need to determine it from mapping the peptide sequence onto its corresponding protein, with the caveat that the

Re: [spctools-discuss] Percolator Error in TPP

Hi Gabby, So since Percolator is not actually running, it just means that the interface is confused. On that page where you see the command list, click on "View" (instead of "Kill Job"), and at the bottom of the page that comes up you will find a small link (at the end of "If your commands have

Re: [spctools-discuss] Percolator Error in TPP

Hello, Is this running on your local machine? If so, you can see if Percolator is still running by either opening the Task Manager (if on Windows) or executing the "ps" command (in Linux). Most likely, the command might have timed out due a very long running time, and the interface (Petunia) is

Re: [spctools-discuss] Kojak File not Found

Hi Lindsey, It seems that Kojak did not finish successfully, and it may be the reason why there is no output file. If you scroll down in the command-line output sub-window (the one in your screenshot, just scroll down more), you should be able to see diagnostic messages that may be helpful in

Re: [spctools-discuss] TPP 5.2 in Ubuntu 18.04 not showing plots/images in PepProphet nor ProtProphet models

Hello Alejandro, Can you share the html source? The most likely culprit is that it has the wrong location of the javascript files. It may also be the case that if you re-installed TPP after you generated the models files, they may need to be updated. The simplest way to do this is to delete

Re: [spctools-discuss] Re: Query related to Lorikeet viewer PTMprophet results in TPP

Hello, It seems that Lorikeet is unable to find the mzML file to extract and display the spectrum. Did you move the files after you conducted the analysis? If you look at the bottom of your screenshot, you can see that the file must be located under "/proteomics/jpanga/." Can you confirm

Re: [spctools-discuss] Failed, error code 256 when I want to run LIBRA with TPP

Hello Cindy, Please note that raw to mzML conversion via the msconvert program only works on Windows systems. Once the file is in the mzML format, you can carry on with analysis on Linux. Cheers, --Luis On Thu, Feb 20, 2020 at 4:48 AM Cindy Dieryckx wrote: > Hello, > > Thanks a lot but now,

[spctools-discuss] TPP @ ASMS 2019 -- booth #118 + Tuesday Workshop

ojak 2.0: New features for the analysis of cross-linked proteins * Michael Hoopmann *MP 044* - * End-to-End Integration of Known Variants and Modifications from PEFF into the Trans-Proteomic Pipeline for Enriched MS/MS Sequence Determination* Luis Mendoza *MP 417 * - *C

Re: [spctools-discuss] Re: StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0)

), while making a backup of the file you have, just in case. Let us know how it goes, and if you find anything else that needs out attention. Cheers, --Luis On Mon, Mar 25, 2019 at 11:27 AM Luis Mendoza < luis.mend...@systemsbiology.org> wrote: > Hi Jason, > > Thanks for the re

Re: [spctools-discuss] Re: StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0)

Hi Jason, Thanks for the report. It seems that the ProtXMLViewer has not been updated to handle dSIn. I'll update this soon and send you a patch. And will be included with our next release, 5.2.1. --Luis On Mon, Mar 25, 2019 at 10:32 AM Jason wrote: > Ok, I can confirm that running

Re: [spctools-discuss] StPeter ERROR: Unknown modification: C[158]

Hello, You can now download a new version of TPP (5.2) which includes the fix to this issue. https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v5.2%20%28Flammagenitus%29%20rev%200/ Cheers, --Luis On Thu, Feb 21, 2019 at 12:19 PM Goutham Vasam wrote: >

[spctools-discuss] TPP 5.2.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 5.2.0 "Flammagenitus". We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 5.2.0. The software is available for Windows as well as Linux from all the usual locations (please see the section

Re: [spctools-discuss] Libra quantification for TMT 11-plex

Hello Rachel, The only potential issue when making your own condition file is to make sure that the isotopic impurity correction factors are correctly entered in the matrix. You also have to add the 11th channel under the and tags, but this should be straightforward. We are adding TMT-11

Re: [spctools-discuss] convert prot.xml to EXCEL with biocontainers/tpp

Hi Robert, As you may have noticed, we have been phasing out the old protXML viewer (and associated helper scripts) in favor of a new, faster, and more modern one. We have implemented the majority of the old functionality into the new one (and much more!), so we have decided to retire the old

Re: [spctools-discuss] TPP on linux command line

Hi Chris, Once you run a command, you can see the exact command line that was run on the Job Output window (after the "EXECUTING:" string). You can also view old commands, as long as their output has not been deleted. Hope this helps, --Luis On Wed, Aug 8, 2018 at 12:48 PM, Chris Waizenegger

Re: [spctools-discuss] QualScore cannot be found anywhere:(

Hello Flora, The QualScore code can be found on our open online repository at: https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/qualscore/ That being said, we have not updated it in some time, and have heard reports that it might not be compatible with recent versions of Java. It is on

[spctools-discuss] TPP @ ASMS -- booth #203 + Wednesday Workshop

its future. Lastly, we will be presenting several posters: -- David Shteynberg: "DISCO: TPP Software Tool to Enable Exploration of Light and Dark Molecular Universes in DIA Experiments" (MP 138) -- Dave Campbell: "Development of Ion Library assessment tools in SWATHAtlas" (MP 141)

Re: [spctools-discuss] Re: No prot-MODELS

Hi Heeyoun, Does it seem that the file is complete when you open it in the ProtXMLViewer? (can you see the last protein group, for example?) If so, maybe there is an issue with the script that generates the models html page. Are you able to share the interact.prot.xml file so I can test it

Re: [spctools-discuss] Re: No prot-MODELS

Hello, The MODELS.html file should be auto-generated when you open the ProtXMLViewer (if one does not exist). If for some reason the models file already exists but is somehow not displaying or is corrupt/broken, the easiest thing to do is to delete that models file and re-open the ProtXMLViewer.

Re: [spctools-discuss] Index mzXML file error

Hello Pavel, This is happening because the index of file 1.mzXML is valid and thus a new file is not created. If the index is incorrect or missing, then a new file is created. We will update the user interface to make this more clear and avoid giving the impression of an error. Thanks for the

Re: [spctools-discuss] X!tandem stops after a few searches

Great! Thanks for the update and glad that it works. --Luis On Mon, Feb 12, 2018 at 9:48 AM, Volkix wrote: > Hi again, > > As Luis suggested it turned out to be a server timeout issue and solved as > Luis guided. I also installed the ubuntu 16.04 and TPP on it. There is a >

Re: [spctools-discuss] X!tandem stops after a few searches

Hi Volkan, In Windows you will want to edit this file: C:\TPP\conf\httpd-tpp.conf . Look for this line, and change the timeout to the desired number of seconds: Timeout *18000* Please note that you will need to *restart *the Apache webserver for any changes to take effect. You could also

Re: [spctools-discuss] X!tandem stops after a few searches

Hi Volkan, This may be a webserver timeout issue; how long do the searches run before they seem to stop? The easiest workaround is to simply run in batches of 5-10 files. Another option is to set the webserver timeout to a longer value. And yet another is to write a script that will do your

Re: [spctools-discuss] Re: Problem with xinteract/peptide prophet

Hello, How did you determine the quality of the XTandem results? How many spectra do you get below an Expect score of 0.01? Is this your own data? As for the parameters, you very likely will want to change the default values that are included in TPP, and that may be the reason for the observed

Re: [spctools-discuss] Use of XPRESS intensities in Peptide/ProteinProphet and XPRESS settings for high-res MS TPP 5.1

Hi Alejandro, You can expect this feature for the next release of TPP (or you can get it now by compiling from our latest code tree). Cheers, --Luis On Thu, Nov 23, 2017 at 4:12 AM, Alejandro wrote: > Hi Luis, > > Thank you very much. I'm already testing it and for a

Re: [spctools-discuss] How to use PeptideProphet with a pepxml file as its input argument?

Hello, It looks like you are compiling a very old version of PeptideProphet, as we no longer use or maintain those executables. For the latest version with full support of Comet results (among others), please use PeptideProphetParser from the latest TPP -- you can just type that into the

Re: [spctools-discuss] TPP 5.X removed NOPLOT, but xinteract appears to not have been updated for the change

Hi Jon, Since the default for ProteinProphet is to not produce png data plots, no option is needed to achieve this. There is no longer a NOPLOT option. Please note that these graphical models are being written to the corresponding -MODELS file (auto-created when running xinteract and/or

Re: [spctools-discuss] TPP_5.1.0

Hello, Please try to follow the instructions we have posted here (for 5.0, but should be applicable to 5.1) -- and please pay close attention to the gcc version requirement for building the external dependency of pwiz and boost: http://tools.proteomecenter.org/wiki/index.php?title=TPP_

Re: [spctools-discuss] TPP 5.X removed NOPLOT, but xinteract appears to not have been updated for the change

Hi Jon, We'll look into removing that option from xinteract. Are you able to run your pipeline without invoking the "t" option? Cheers, --Luis On Mon, Dec 11, 2017 at 4:18 PM, wrote: > Hi, > > First time here. I noticed that since TPP 5.0, the NOPLOT option was > removed: >

Re: [spctools-discuss] Use of XPRESS intensities in Peptide/ProteinProphet and XPRESS settings for high-res MS TPP 5.1

Hi Alejandro, You can download the updated Xpress and interfaces from our dev staging site: https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v0.0%20%28Development%29/ Unzip XpressIntensityUpdate.zip, and place XPressPeptideParser.exe under the

Re: [spctools-discuss] TMT Quant with Libra (Ignore/rescue zero values i.e. large ratios & select/de-select quantified peptides)

Hi Adam, Do those psm's have a reported Libra result in the PepXMLViewer? Do all of these peptides come from a single run? Or is this a combined analysis of multiple runs? Also might want to try using 5.1 (if not already doing so) in case there was a bug that got fixed. Cheers, --Luis On

Re: [spctools-discuss] Use of XPRESS intensities in Peptide/ProteinProphet and XPRESS settings for high-res MS TPP 5.1

Hi Alejandro, The misreported intensity ratios was a bug when using the -L or -H options in XPRESS. We have fixed this, as well as added support for those fields in PepXMLViewer and Petunia. If you are building from sources, simply build revision 7683, or let us know if you would like Windows

Re: [spctools-discuss] Problem with Ubiquitination tag on spectrast

Hello Marine, Unfortunately, you can only find these modifications by looking at the source code of SpectraST, specifically, this file: (e.g. find "GlyGly") https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/src/Search/SpectraST/Peptide.cpp Also, from a quick

Re: [spctools-discuss] Use of XPRESS intensities in Peptide/ProteinProphet and XPRESS settings for high-res MS TPP 5.1

Hello Alejandro, We will add these columns to the PepXMLViewer for the next release; I can let you know when we have a pre-release version if you would be interested in testing it. I am not sure why the ratios are not being correctly calculated; we will have a look and try to fix as well for the

Re: [spctools-discuss] TMT Quant with Libra (Ignore/rescue zero values i.e. large ratios & select/de-select quantified peptides)

Hi Adam, A further requirement is that the peptide be matched to the protein via a weight > 0.5 (i.e. used in the calculation of the protein probability as assigned by ProteinProphet). Let us know if this is not the case and we can delve into it further. Cheers, --Luis On Fri, Nov 10, 2017 at

Re: [spctools-discuss] TMT Quant with Libra (Ignore/rescue zero values i.e. large ratios & select/de-select quantified peptides)

Hi Adam, Hard to tell exactly without looking at your file. One thing to note is that Libra will only use psm's with PeptideProphet probabilities > 0.5; it does not take into account iProphet probabilities (yet). Maybe this explains some of the ones that are missing? Cheers, --Luis On Fri,

Re: [spctools-discuss] TMT Quant with Libra (Ignore/rescue zero values i.e. large ratios & select/de-select quantified peptides)

I forgot to add that once the protein quantitation is done, Libra will also produce a "quantitation.tsv" file that you can use downstream for re-evaluating protein ratios with any statistical(s) test you wish -- say in R, Excel, etc. The file structure is fairly straightforward: protein ratios

Re: [spctools-discuss] TMT Quant with Libra (Ignore/rescue zero values i.e. large ratios & select/de-select quantified peptides)

Hi Adam, We have plans to add some of these features to Libra as well as others, but none are ready at the moment. One thing you could try is to select to normalize against the sum of the reagent profiles (instead of selecting a channel to quantify against) -- this should give you a value for

Re: [spctools-discuss] Running StPeter on peptides labeled with TMT (as fixed mod in Comet) Error in Quant

Hi Adam, Thank you for your report. We have now modified how StPeter handles modifications. If you build TPP from sources, you can see this in rev 7675. Or let me know if you require a Windows executable, and we'll post it on our files section. Cheers, --Luis On Thu, Nov 9, 2017 at 8:51

Re: [spctools-discuss] Documentation for Linux version of TPP?

Hi Owen, Do you know if they also installed and configured TPP to be used with Apache? (or whichever web server is running on that machine) If so, you should be able to follow the GUI tutorial, as well as interact with the data (all of our viewers are web-based). The UI (called Petunia) will

Re: [spctools-discuss] running a pepXML output from Myrimatch to parse through peptide-PROPHET

Hello Trayambak, The input filename has the wrong extension. If you see the full name on the last screenshot, it ends in* .pep.xml.pepXML*. It has to be renamed so that it ends in *.pep.xml* for the interface to recognize it. Hope this helps, --Luis On Thu, Nov 2, 2017 at 3:00 PM, Trayambak

Re: [spctools-discuss] x tandem search Command FAILED RETURN CODE:65280

Hello, Were you able to get this search to work? One issue to note is the following: Failed to open: "C:\Inetpub\wwwroot\ISB\data\parameters\isb_default_input_kscore.xml" Make sure that your Tandem parameters are set correctly, including the location of the auxiliary files. Cheers, --Luis

Re: [spctools-discuss] Re: TPP v5.1.0 Installation Windows Server 2012

Hi Adam, Glad that you solved the issue, and thanks for reporting back. --Luis On Wed, Nov 8, 2017 at 5:05 PM, Adam R wrote: > Figure it out. Posting here as a resource: > > I tried to install the 3.5 SP1 installer required for ProteoWizard but > that wasn't working.

[spctools-discuss] TPP 5.1.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 5.1.0 "Syzygy" We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 5.1.0. The software is available for Windows as well as Linux from all the usual locations (please see the section below,

Re: [spctools-discuss] TPP 5.0 compilation on CentOS fails

Thanks for finding and reporting this, Jimmy. We'll make a note and attempt to fix by next release. On Wed, Jun 14, 2017 at 1:35 PM, Jimmy Eng wrote: > Just to give some closure to this in case anyone else comes across this > error, the solution was to remove any trailing

Re: [spctools-discuss] TMT 8-plex Libra Condition File Parameters

Hello Linh, Do you have a Lot Number for your TMT kit? If so, you might be able to find the reported ion isotopic distribution factors via the Thermo website -- or contact your rep. One such example (TMT-10) : https://tools.thermofisher.com/content/sfs/COAPDFs/2015/OJ185435_90110.pdf Otherwise,

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