Re: [spctools-discuss] Seeking help regarding peptide prophet and decoy mode

o > MSStatsTMT - see here https://groups.google.com/g/msstats/c/aINhWMKt2Co) > While MSStatsTMT has converters for other SW like Maxquant and PD, I kind > of like TPP, so trying to establish a proper workflow for my fractionated > TMT data. > > Thanks again, > Debojyoti > > O

Re: [spctools-discuss] Running MSfragger search in TPP 7.0

Hi Zeyu, Thanks for your question and for your interest in the TPP. Yes I use MSFragger in the TPP and I did run into this exact problem last week. It required me to install java 9 jdk that I downloaded and installed from oracle. I then had to make sure that the windows PATH pointed to the

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

dress number > incorrectly. Everything loading and running now with proper style sheet. > > Thanks for the help in tracking this down. > > Regards > Robert > > On 17 Apr 2024, at 7:59 AM, 'David Shteynberg' via spctools-discuss < > spctools-discuss@googlegroups.c

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

s. > No not serving any other sites from this server. > > Regards > Robert > > On 17 Apr 2024, at 12:53 AM, 'David Shteynberg' via spctools-discuss < > spctools-discuss@googlegroups.com> wrote: > >  > This seems to be a configuration issue but I am not sure where,

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

format error: AH01241: exec of >> '/usr/local/tpp/cgi-bin/tpp_gui_config.pl' failed >> >> [Tue Apr 16 13:08:10.934745 2024] [cgid:error] [pid 841395:tid >> 140546200757824] [client ::1:38680] End of script output before headers: >> tpp_gui_config.pl >> On Tu

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

or. >> >> More information about this error may be available in the server error >> log. >> >> [Tue Apr 16 13:08:10.934308 2024] [cgid:error] [pid 841488:tid >> 140546230744960] (8)Exec format error: AH01241: exec of >> '/usr/local/tpp/cgi-bin/tpp_gui_con

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

/html > REQUEST_SCHEME = http > SEQ2MS_DEFAULT_MODEL = _SEQ2MS_DEFAULT_MODEL_ > QUERY_STRING = > SERVER_ADMIN = [no address given] > HTTP_SEC_FETCH_SITE = none > WEBSERVER_TMP = /tmp > SERVER_PROTOCOL = HTTP/1.1 > HTTP_UPGRADE_INSECURE_REQUESTS = 1 > HTTP_SEC_FETCH_DEST

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

. Good luck! -David On Apr 15, 2024, at 7:01 AM, David Shteynberg < david.shteynb...@isbscience.org> wrote: Hi Robert, Thanks for trying to install and use TPP on Ubuntu. It seems the webserver is somewhat misconfigured for tpp on your system. Can you share the site.mk file that yo

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

Hi Robert, Thanks for trying to install and use TPP on Ubuntu. It seems the webserver is somewhat misconfigured for tpp on your system. Can you share the site.mk file that you are using for this build as this file allows to control the PATHs and URLS used by TPP? Thanks! -David On Mon, Apr

Re: [spctools-discuss] Lib2HTML truncates peptide sequences after modification

gt; > Cheers! > Juergen > > David Shteynberg schrieb am Donnerstag, 11. April 2024 um 02:28:19 UTC+2: >> Hello Juergen, >> >> Thanks for providing the test data. I was able to modify the code to allow >> Lib2HTML to also read the user modifications and d

Re: [spctools-discuss] Re: Lib2HTML truncates peptide sequences after modification

Hello Juergen, Thanks for providing the test data. I was able to modify the code to allow Lib2HTML to also read the user modifications and display the from the HTML page. The prerelease installer that has this feature is available here:

Re: [spctools-discuss] Issue with MSConvert of TPP v7.0.0.

izard\ProteoWizard 3.0.23233.c72ce16\msconvert" [image: image.png] Cheers! -David On Fri, Apr 5, 2024 at 11:07 AM David Shteynberg < david.shteynb...@isbscience.org> wrote: > Hello Nachiket, > > Thanks for your interest in the TPP! The location where proteowizard is &

Re: [spctools-discuss] Issue with MSConvert of TPP v7.0.0.

Hello Nachiket, Thanks for your interest in the TPP! The location where proteowizard is installed on your system is not in your windows system PATH environment variable. Please add the directory where you found msconvert to your PATH environment variable and try running it again. Let us know

Re: [spctools-discuss] TPP 7.0.0 Release is now available

Nitro Butyryl Formyl Gluratylation hydroxyisobutyryl Propionyl Succinyl Trimethyl Deamidated Gln->pyro-Glu Glu->pyro-Glu > On Apr 4, 2024, at 6:59 AM, David Shteynberg > wrote: > > Hello Juergen, > > Thank you for your question and use of TPP! Seq2MS's suppor

Re: [spctools-discuss] Re: TPP 7.0.0 Release is now available

peptides after the modified residue) > was solved? > > Best regards, > Juergen > > > > David Shteynberg schrieb am Samstag, 30. März 2024 um 02:47:30 UTC+1: > >> Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.0.0 >> "Arafel" >>

[spctools-discuss] TPP 7.0.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.0.0 "Arafel" We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 7.0.0. The software is available for MacOS, Windows, Linux, as well as Android from all the usual locations (please see

[spctools-discuss] Bug Discovery in decoyFastaGenerator.pl

Dear TPP Users, We have recently discovered and patched a bug in the TPP tool *decoyFastaGenerator.p*l. The bug manifests by excluding the last sequence from the input protein database from both randomization and output, instead outputting the penultimate protein sequence twice. The next

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

from the last time I ran the data, which worked the > last time. On MassLynx, the intensities look normal as well, with a dome of > increasing intensities over the gradient, typical of bottom up proteomics. Is > there a way to solve this? > > On Wednesday, January 10, 2024 at

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

r inputs! > > Best, > Alex > > On Friday, January 5, 2024 at 1:09:03 AM UTC+1 David Shteynberg wrote: >> Hello Alex, >> >> Thanks for trying the TPP pipeline to solve your proteomics computational >> needs. Sorry, you are having trouble converting and analy

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

Hello Alex, Thanks for trying the TPP pipeline to solve your proteomics computational needs. Sorry, you are having trouble converting and analyzing Waters raw data. Have you tried using the latest version of msconvert to do the conversion to mzML? If you are able to upload your file to an

Re: [spctools-discuss] Hi I cannot access the gui anymore is there something I'm missing

ts a windows, > How do I check which version I have? > > On Tue, 5 Dec 2023 at 14:57, 'David Shteynberg' via spctools-discuss > <mailto:spctools-discuss@googlegroups.com>> wrote: >> Is this windows, linux, mac? Which version of the TPP software did you >> dow

Re: [spctools-discuss] Hi I cannot access the gui anymore is there something I'm missing

or > But how do I check what version I have of TPP? > > Thank you, > Aarthie > > On Mon, 4 Dec 2023 at 17:54, David Shteynberg < > dshteynb...@systemsbiology.org> wrote: > >> Hello, >> >> If you could provide some additional information such as: you

Re: [spctools-discuss] running ASAPratio for SILAC data

gards, Sudarshan > > On Mon, Dec 4, 2023, 2:29 PM 'David Shteynberg' via spctools-discuss < > spctools-discuss@googlegroups.com> wrote: > >> Hello Sudarshan, again! >> >> I was able to update the ASAPRatioPeptideParser.exe tool for your testing >> purpo

Re: [spctools-discuss] Hi I cannot access the gui anymore is there something I'm missing

Hello, If you could provide some additional information such as: your operating system, which version you installed and relevant configuration during installation, that would be helpful in troubleshooting your issue. Thanks! -David > On Dec 4, 2023, at 2:21 PM, Aarthie Senathirajah >

Re: [spctools-discuss] running ASAPratio for SILAC data

files so that zero >>>> intensity peaks in the MS1 data are removed and the MS1 data is >>>> centroided. You can accomplish both of these things using the msconvert >>>> tool. This will help reduce the time requirement to process this dataset. >>>> I

Re: [spctools-discuss] running ASAPratio for SILAC data

a was acquired >> in profile mode >> Compress peak lists for smaller output file >> Write the output as a gzipped file (other TPP tools can read gzipped >> files directly) >> >> On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg < >> dshteynb...@systemsbiolog

Re: [spctools-discuss] running ASAPratio for SILAC data

wrote: > > Hi David, > could you get time to see into my analysis? I need your advice. > Best regards, > Sud > > On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss > <mailto:spctools-discuss@googlegroups.com>> wrote: >> Hello Sudars

Re: [spctools-discuss] sud silac asapratio

You will also need to shared the mzML file containing the data. Thanks! On Wed, Nov 22, 2023 at 4:07 PM sudarshan kumar wrote: > interact_silaccomtwofiles.pep.zip > > > > -- >

Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization

Thanks Longping, I got your files. > On Nov 17, 2023, at 5:21 PM, Longping Fu wrote: > > Dear David, > > I appreciate your swift response. I've compressed the pepXML and mzML files > and uploaded them to Google Drive. You can access them through the following > link: >

Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization

Dear Longping, Maybe you can compress your analysis pepXML and mzML files and post them somewhere so I can replicate the issue locally? Meanwhile, you can try the specifying all variable mods used in the search, when you run PTMProphet by changing the modification string as follows:

Re: [spctools-discuss] XPRESS peak intensity value

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

[spctools-discuss] Re: StPeter error - Could not read spectra

Hey Jason, If you are able to compress the dataset directory and share it I would be happy to troubleshoot this particular issue. Cheers! -David On Thursday, August 31, 2023 at 12:52:42 PM UTC-7 jwi...@gmail.com wrote: > I am trying to process my data using StPeter and am getting the

Re: [spctools-discuss] Navigating peptideSieve Tips/Tricks?

Sure! This was my command: [image: image.png] On Tue, Aug 1, 2023 at 10:48 AM sophie culos wrote: > David, would you be at all willing to post the code that you were using? > I'll give "/" a shot in my path definitions. > > > > On Tuesday, August 1, 2023 at 10:35:

Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides

ely protein candidate. The result of which is recorded in > the "total num peptides" value. In the case of a tie, is the value added > to all possible protein hits or not used? > > Thanks a bunch! > > Brian > -- > *From:* 'Davi

Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides

Best regards, >> Brian >> >> >> >> Brian Hampton >> Proteomics Core Lab >> >> Center for Vascular and Inflammatory Diseases >> >> University of Maryland School of Medicine >> >> BioPark One Rm 307 >> >> 800 West Baltimore

Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides

University of Maryland School of Medicine > > BioPark One Rm 307 > > 800 West Baltimore Street > > Baltimore, MD. 21201 > > (410)706-8207 > -- > *From:* 'David Shteynberg' via spctools-discuss < > spctools-discuss@googlegroups.com> > *Sent:* W

Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides

2023 at 7:27 AM muriell...@gmail.com < murielle.al...@gmail.com> wrote: > Hi David, > > Thank you for such a quick reply! > > I used tpp version 6.2.0 run via a singularity image and I produced the > table by including the EXCELXX option in proteinprophet. > > Cheers, > >

Re: [spctools-discuss] Installer for TPP 6.3.0 does not recognize existence of MS VC++ 2015-2022

Hello Scott, You should be able to get around this issue by unchecking the option to download and install Kojak dependencies during the installation. If that still fails let me know. Cheers, -David On Thu, May 4, 2023 at 9:31 PM Scott Starry wrote: > Due to security restrictions, my company

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

Hello, Generally this message means that you have no PSMs with good likelihoods of being correct in this analysis set. There are a few "usual suspect" reasons for why you would not observe any PSMs with non-zero probabilities among your results. 1. Poor quality data (e.g. empty sample) 2.

Re: [spctools-discuss] Error running xinteract on Kojak results using latest Docker image

Hi Mike, With Kojak data the peptide length is meaningless and recorded as zero in the pepXML. The default parameters of xinteract use min peptide length of 7 which invalidates all results in this file. You have to run with min peptide length of zero when processing Kojak data: xinteract -l0

Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML

hank you. I concur deleting those characters resolves the issue. >> >> My colleague Gabriel actually was running the tutorial test. I will ask >> him to chime in if he did anything other than follow the steps given. >> >> On Friday, June 10, 2022 at 12:03:08 PM UTC-5 Da

Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML

test. I will ask > him to chime in if he did anything other than follow the steps given. > > On Friday, June 10, 2022 at 12:03:08 PM UTC-5 David Shteynberg wrote: > >> Hello again Malcolm, >> >> There are several of these non-ascii characters in the protXML file that >&g

Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML

Hello again Malcolm, There are several of these non-ascii characters in the protXML file that you sent. After I removed them I was able to open the file in ProtXMLViewer. Also the syntax errors from tpp2mzid went away (although I wasn't able to convert your file without the associated pepXML

Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML

Hi Malcolm, The message is complaining about line 148 of the pepXML file which look like this: Apparently this protein entry in your database has a non-ascii character in the descriptions of this protein. Can you please share this database so I can examine this protein entry or can you check

Re: [spctools-discuss] getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl

the access log: >>> >>> 127.0.0.1 - - [08/Jun/2022:17:08:39 -0500] "GET /tpp/cgi-bin/tpp_gui.pl >>> HTTP/1.1" 403 224 "-" "Mozilla/5.0 (X11; Linux x86_64; rv:91.0) >>> Gecko/20100101 Firefox/91.0" >>> >>> On Wedn

Re: [spctools-discuss] getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl

It sounds like you are making progress get this installed and running. Can you check the apache error logs to see if they hold the next clue? Thanks, David On Wed, Jun 8, 2022, 4:25 PM Malcolm Cook wrote: > I just finished building and installing TPP under centos7 > > Following Testing the

Re: [spctools-discuss] stuck with problem making tpp

Also, I wouldn't recommend using make -k because then you get errors with linking of the sort you are seeing because prerequisite dependencies are not being built properly so downstream linking of applications to dependencies fails. Can you send the actual errors that are generated when you run

Re: [spctools-discuss] stuck with problem making tpp

Dear Malcolm, Sorry you are having trouble building the TPP on centos 7. There are many ways you can use the TPP both on the cloud and locally in virtual machines which would not require you to build the tools from source. Nevertheless, the latest release of the TPP has been updated to the

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

Hi Malcolm, Thanks for your interest in the TPP. I think your url has a mistake in it. Please try the following command: svn checkout http://svn.code.sf.net/p/sashimi/code/tags/release_6-1-0 Cheers, -David On Tue, Jun 7, 2022 at 3:44

Re: [spctools-discuss] TPP 6.1.0 rc9 Missing module in Perl installation

Dear Juergen, Thank you very much for pointing this out. We will be sure to have this patched for the official release. Cheers, -David On Fri, Apr 22, 2022 at 6:43 AM Juergen Bartel < juergen.bar...@uni-greifswald.de> wrote: > Dear TPP developers, > > I tried the release candidate of TPP 6.1

Re: [spctools-discuss] Libra on MS3-based TMT quantification

elp! > > Shagun > > On Tuesday, April 5, 2022 at 3:09:59 PM UTC-4 David Shteynberg wrote: > >> Hello Shagun, >> >> Thank you for sharing your complete dataset. I still found the following >> in the conditions file you included: >> TMT10_VB297695

Re: [spctools-discuss] Libra on MS3-based TMT quantification

wrote: > The zip folder for the files can be found here: > https://drive.google.com/drive/folders/1hnR2igUXM_K-Pld2xspikeu_xnLGUdMc?usp=sharing > > Let me know if you have any issues. > > Best > Shagun > > On Friday, March 25, 2022 at 1:34:57 PM UTC-4 David Shteynberg wr

Re: [spctools-discuss] Tandem2XML all-15N issue

f I can be of further > assistance. > > Farshad > > On Thu, Feb 24, 2022 at 2:32 PM David Shteynberg < > david.shteynb...@isbscience.org> wrote: > >> Dear Farshad, >> >> Yes this looks like something that can be corrected. The fix would use >> the u

Re: [spctools-discuss] Libra on MS3-based TMT quantification

gun > > On Friday, March 25, 2022 at 6:02:55 PM UTC-4 Shagun Gupta wrote: > >> Hi David >> >> Will do so, thank you! That makes a lot of sense. I have also added the >> mzXML files but this might be the cause of the discrepancy I see! >> >> Thanks >&g

Re: [spctools-discuss] Libra on MS3-based TMT quantification

I can share the > pep.xml's and Libra condition file that way? > > -Shagun > > On Friday, March 25, 2022 at 11:00:38 AM UTC-4 David Shteynberg wrote: > >> Hello Shagun, >> >> Thank you for your email and interest in the TPP. I have recently been >> comp

Re: [spctools-discuss] Libra on MS3-based TMT quantification

Hello Shagun, Also please include your mzML files, which contain the actual data that Libra quantifies. Thanks! -David On Fri, Mar 25, 2022 at 10:34 AM David Shteynberg < david.shteynb...@isbscience.org> wrote: > Please place your files on a shared drive and send me a link. > >

Re: [spctools-discuss] Libra on MS3-based TMT quantification

March 25, 2022 at 11:00:38 AM UTC-4 David Shteynberg wrote: > >> Hello Shagun, >> >> Thank you for your email and interest in the TPP. I have recently been >> comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that produced >> by TPP's Libra. As fa

Re: [spctools-discuss] Libra on MS3-based TMT quantification

Hello Shagun, Thank you for your email and interest in the TPP. I have recently been comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that produced by TPP's Libra. As far as I can tell, when I run and compare the quantities (intensities) they are mostly the same between Libra

Re: [spctools-discuss] Tandem2XML all-15N issue

Dear Farshad, Yes this looks like something that can be corrected. The fix would use the user-specified mass modification and only when that is not available fall back to the hard-coded value. I can make the change but would need your data so I can replicate the problem. Are you able to

Re: [spctools-discuss] Re: TPP Comet search time-out

Hi Will, Thanks for posting your question. This is due to a timeout setting in the webserver. Thankfully there is a simple fix: https://groups.google.com/g/spctools-discuss/c/ZNXMkdB9Y48/m/TYcnPIHgBwAJ In Windows the steps are : 1. Edit this file: C:\TPP\conf\httpd-tpp.conf . 2. Change the

Re: [spctools-discuss] PTMProphet flags

Dear Pedro, Sorry about the delay in my response to your query. I am not sure what version of PTMProphet you are using, we are currently on TPP 6.0.0 official release (6.1.0 available as a release candidate.) Here is some more information about the options you are interested in: *LABILITY

Re: [spctools-discuss] Precursor Intensity after Comet search

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: >

Re: [spctools-discuss] TPP 6.0 Libra Error

phet 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:

Re: [spctools-discuss] TPP 6.0 Libra Error

ded, 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: >

Re: [spctools-discuss] TPP 6.0 Libra Error

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 >>

Re: [spctools-discuss] TPP 6.0 Libra Error

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

Re: [spctools-discuss] PTMProphet and best localization score

Hi Niko, Thanks for your question and interest in the TPP. The PepXMLViewer.cgi tool can be used to display, filter and export pepXML data, including PTMProphet processed results. PTMProphet computes several statistics for each PSM and for each PTM analyzed: Mean Best Probability -- is the

Re: [spctools-discuss] xinteract (TPP v5.2.0) not detecting any spectra from comet output

Hi Damian, Unfortunately, TPP 5.2.0 is not forward compatible to comet 2020. We are working on the 6.0.0 release and have a couple of release candidates available. I will post another rc tomorrow. Cheers, David On Sat, Apr 24, 2021, 9:09 AM dfermin wrote: > Hello > > I performed a search

Re: [spctools-discuss] PTMProphet command failure (for larger datasets?)

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 candidat

Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

l%7C342d2db781c2443416b108d8febfbc70%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637539447557029368%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=LBdAB3QsH9rUxvNKMwKjOKYDbQXFxma9dREKgS5siWQ%3D=0> > Thanks, > Oded > > > > On Tuesday, 13 April 2021

Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

pbox.com/t/Yld0ZBWhsuFajeLj >> The link is valid for 7 days. >> Many thanks, >> Oded >> >> On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote: >> >>> I don't mind taking a crack at it over vacation. Please let me know >>> where I can

Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

either the raw file or the search results. > Enjoy your vacation. > Thanks, > Oded > On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote: > >> Hi Oded, Which release candidate are you referring to? The earlier >> candidates may have a bug that is corrected in

Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

Hi Oded, Which release candidate are you referring to? The earlier candidates may have a bug that is corrected in a later version. If you can share some data and specifics about the missing PSMs I can run it here and troubleshoot the problem. Thanks! David P.S. I am on vacation this week so

Re: [spctools-discuss] PTMProphet command failure (for larger datasets?)

sion 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 >>

Re: [spctools-discuss] job end with error when following PTMprophet tutorial

o.pep.xml > > [image: command.png] > > Best, > Panyue > > On Wed, Mar 10, 2021 at 12:54 AM 'David Shteynberg' via spctools-discuss < > spctools-discuss@googlegroups.com> wrote: > >> Hello again, >> >> I downloaded the code from sourceforge and repl

Re: [spctools-discuss] job end with error when following PTMprophet tutorial

or doesn't work for you. Thanks! -David On Tue, Mar 9, 2021 at 9:33 PM David Shteynberg < david.shteynb...@isbscience.org> wrote: > It should only take a few minutes to run the code. Perhaps there is a > permissions issue to execute that file on your computer. Normally the > insta

Re: [spctools-discuss] job end with error when following PTMprophet tutorial

yue > [image: Updatepaths.png][image: JobRun.png] > > On Tuesday, March 9, 2021 at 4:34:01 PM UTC-5 David Shteynberg wrote: > >> Hello Panyue, >> >> I test the updatePaths.pl and found some problems with it correcting >> paths to directories on other drives on wind

Re: [spctools-discuss] Error in fitted models for MSgf+ search

gt; Apologies. > > Please find the database with decoy > > https://drive.google.com/file/d/18ijaNWgmIompoJ0m99V0bCD4j54hXRlR/view?usp=sharing > > ASIF > > > On Wednesday, February 10, 2021 at 10:55:02 AM UTC+11 David Shteynberg > wrote: > >> It appears you forgot

Re: [spctools-discuss] Error in fitted models for MSgf+ search

ipro.pep.xml). > > > https://drive.google.com/file/d/1rULaUtY9j2Ke7N6Z_hIa_a_JyY3admvj/view?usp=sharing > > ASIF > > > On Wednesday, February 10, 2021 at 8:48:19 AM UTC+11 David Shteynberg > wrote: > >> You can compress the directory and post your dataset in the

Re: [spctools-discuss] Tutorial DIA Analysis

Dear Cethgar, Thanks for pointing that out, we have updated the link. Please try again and let us know should you have any additional questions or find other issues. Cheers, -David On Mon, Jan 25, 2021 at 11:16 AM Cethgar XXX wrote: > > Hi, > I wanted to check out the tutorial " DIA Analysis

Re: [spctools-discuss] When to use "Decoy hits to pin down negative distribution" in PeptideProphet

ush > > On Tuesday, January 19, 2021 at 2:59:56 PM UTC-5 David Shteynberg wrote: > >> Dear Soroush, >> >> This option makes use of the TPP's semi-supervised learning mode, which >> can be used in conjunction with semi-parametric mode, at the user's >> discre

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

> XML output file? > > Thanks a lot in advance! > > G > > Il giorno martedì 19 gennaio 2021 alle 20:53:57 UTC+1 David Shteynberg ha > scritto: > >> Dear Giangiacomo, >> >> Thanks for trying the TPP and reporting the problem. TPP uses the >> prot

Re: [spctools-discuss] When to use "Decoy hits to pin down negative distribution" in PeptideProphet

Dear Soroush, This option makes use of the TPP's semi-supervised learning mode, which can be used in conjunction with semi-parametric mode, at the user's discretion. Until now, some search engines supported by TPP analysis could only be modeled by PeptideProphet using semi-parametric and

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

Dear Giangiacomo, Thanks for trying the TPP and reporting the problem. TPP uses the proteowizard's msconvert tools for this step. You can remedy the problem by either upgrading to a newer version of proteowizard's msconvert tool or use --ignoreUnknownInstrumentError option with your current

Re: [spctools-discuss] iprophet is search showing blank page

Hello Sudarshan, Did the program report any messages when it ran? Are you certain that the PeptideProphet input going to iProphet contains PSMs with non-zero probabilities? Thanks, -David On Mon, Dec 14, 2020 at 9:58 PM sudarshan kumar wrote: > I have analyzed a data file using peptide

Re: [spctools-discuss] Select only top matching protein in spectrast

Hi Shubham, Thanks for using the TPP tools and submitting your question here. A peptide may map to more than one protein, when this happens the TPP will usually map each peptide to all proteins where it can occur. There are some exceptions to this such as I/L substitutions and protein specific

Re: [spctools-discuss] command "C:/TPP/bin/PeptideProphetParser" failed

Use Jimmy's solution until the next release. On Wed, Dec 2, 2020 at 11:41 AM Asif Ahmed wrote: > I am using the windows version, > any suggestion for that? > > On Thu, 3 Dec 2020 at 6:30 am, 'David Shteynberg' via spctools-discuss < > spctools-discuss@googlegroups.com>

Re: [spctools-discuss] command "C:/TPP/bin/PeptideProphetParser" failed

source forge > website, but could not find it. > > On Thu, 3 Dec 2020 at 5:58 am, 'David Shteynberg' via spctools-discuss < > spctools-discuss@googlegroups.com> wrote: > >> I have updated PeptideProphetParser so that it CAN run with the new >> version of Comet. You wi

Re: [spctools-discuss] command "C:/TPP/bin/PeptideProphetParser" failed

I have updated PeptideProphetParser so that it CAN run with the new version of Comet. You will have to get it from the TPP SVN repository. On Wed, Dec 2, 2020 at 10:50 AM Jimmy Eng wrote: > Stick with Comet 2019.01.5. In version 2020.01.0, I deprecated the > "deltacnstar" score in Comet and

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

individual characters >>> unique to either the headers or the sequences in 10OV, so I don't think >>> there's an individual character messing things up.) >>> >>> On Thursday, October 22, 2020 at 3:49:18 PM UTC-4 David Shteynberg wrote: >>> >>>>

Re: [spctools-discuss] Linux Build Error

Hi Nathan, These are some bugs in the TPP externals that have been fixed in the more recent versions of the code. You can either pull the offending files from a more recent version of the code, use an up-to-date trunk version of the code (and report any bugs you find ;), or wait until we make

Re: [spctools-discuss] DIA to mzML question

Dear Jane, I cannot help you with the demultiplexing, because I have not used that feature before in MSConvert. But if you do manage to get a regular DIA mzML file out of the conversion you can use the DISCo tool available in the TPP under Tools->DIA->Extract MS2 Fragments that will generate a

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

it's a problem with my spectra or my database - will let you > know how that turns out! > > Emily > > On Thursday, October 22, 2020 at 3:09:29 PM UTC-4 David Shteynberg wrote: > >> Hi Emily, >> >> I analyzed the search results that you sent and I am seein

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

October 20, 2020 at 1:30:44 AM UTC-4 David Shteynberg wrote: > >> Hi Emily, >> >> I got the data and now I am trying to understand how you are running the >> analysis. Can you please describe those steps? >> >> Thank you, >> -David >> >>

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

tting it transferred to Drive, so it might >> take a little while, but I'll be in touch! >> >> On Tuesday, October 13, 2020 at 3:08:44 PM UTC-4 David Shteynberg wrote: >> >>> Hello Emily, >>> >>> If you are able to share the dataset includin

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

Hello Emily, If you are able to share the dataset including the pepXML file and the database I can try to replicate the issue here and try to troubleshoot the sticking point. Thanks, -David On Tue, Oct 13, 2020 at 11:15 AM Emily Kawaler wrote: > Hello, and thank you for your response! It

Re: [spctools-discuss] Converting Orbitrap Eclipse files to mzML

Hi Laura, Can you try downloading the latest version of msconvert and replacing your copy in C:/TPP/bin or where you currently have it installed? Once you get an mzML file you can copy it to your TPP data directory and run the search, validation, etc. Let us know how it goes. Cheers, -David

Re: [spctools-discuss] Crosslink FDR from PeptideProphet

Hi Lindsey, PeptideProphet will generate a separate FDR prediction table for each type of Kojak result it analysed, and all three should be in the pepXML file. The three types of Kojak hits are unlinked "n/a", self-linked "loop" and cross-linked "xl".PeptideProphet generates a separate model

Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio

21:23:55 UTC+2 Alastair Skeffington wrote: > >> Hi David, >> >> Ah sorry - my mistake. Here's a new link with a tarball including the >> mxXML files. >> >> https://we.tl/t-UnX74n4qod >> >> Many thanks! >> Alastair >> >> >>

Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio

for offering. I've put two example pairs of files here: >> https://we.tl/t-cVDD1MVDOr >> >> For each sample there is a light 'L' version of the search results and a >> heavy 'H' version. I've also included the search database (based on some >> PacBio data some I'm afraid i

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