Re: [spctools-discuss] Peptide prophet showing all zero probability

also required are your search params and db On Thu, Jul 25, 2024, 5:14 AM sudarshan kumar wrote: > 20240417_AN_171_POS_LCMSMS_00.shrunken.mzML > > > > On Tue, Jul 23, 2024 at 10:16 AM David Shteynberg < >

Re: [spctools-discuss] Peptide prophet showing all zero probability

Can you compress the mzML file, the search database and your search together and reshare? I will need at least those file to try to reproduce your process. Cheers! On Wed, Jul 24, 2024, 2:19 AM sudarshan kumar wrote: > > 20240417_AN_171_POS_LCMSMS_00.mzML >

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

Hello Zeyu, Would you mind installing the latest update and report back if you still have an issue here? Thanks, -David On Thu, Jul 18, 2024 at 1:35 PM Zeyu Wang wrote: > Hi David, > > Sorry for the late reply. Later, I just left the computer running on > E-cores, which took longer. Now I

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

Hi Zeyu, Thanks for testing this! I recompiled another executable that should use more of the CPU during the search. Can you please test it to see if this suits your needs? Naturally, if you set the number of threads too high it might degrade the overall performance of your machine during the

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

Hello Zeyu, Sorry I don't know the answer to your question but if it helps I corrected the issue you identified in the previously distributed version compiled with gcc for the TPP distribution installer. I placed the gcc compiled version of Kojak.exe here:

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

Hello again, After a bit of digging I found that this is likely caused by a bug in the current TPP compiled and distributed version of Kojak that will have to be corrected for the next release. Meanwhile you should be able to download and use the official Kojak build available here:

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

Hello Zeyu, Thanks for your interest in TPP and Kojak. Yes we maintain and use Kojak in the latest release. To help us troubleshoot this problem, would you mind sharing the parameter file used in your test? Thank you! -David On Fri, May 24, 2024, 12:28 AM Zeyu Wang wrote: > Hi, > > Are

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

Here is the best reference describing iProphet in detail: https://pubmed.ncbi.nlm.nih.gov/21876204/ iProphet starts with PeptideProphet probabilities at the "PSM-level" (always model-based) and computes the probabilities at the "peptide-level." It always produces one result per spectrum (whether

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

This seems to be a configuration issue but I am not sure where, likely in the server. It appears you are running apache 2.4.x (same as I, on my phone ubuntu emulator ;) which is in configured by http-2.4-tpp.conf. This file should be first configured by site.mk at make install. You should not

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

Can you seen if you can access the server at: 127.0.0.1:10401/tpp or 127.0.0.1:10401/tpp/cgi-bin/tpp_gui.pl Thanks! On Mon, Apr 15, 2024, 11:50 PM Robert Willows wrote: > one more piece of puzzle. > The httpd-tpp.conf has: > ## Set the TPP's environment variables > SetEnv TPP_HOME

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, I think I see the problem. TPP_BASEURL and TPP_DATAURL should be relative, no start with '/', try changing your site.mk to : INSTALL_DIR = /usr/local/tpp TPP_DATADIR = /data TPP_BASEURL = tpp TPP_DATAURL = tpp/data TPP_PORT = 10401 Then you will need to make all and make install

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] 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.

Natchiket, Alternatively to setting the environment PATH, you should be able to run msconvert on the commandline by using the full path to the executable instead, (and remember to include the quotes!) This is the full path on my system, and likely also on yours: "c:\Program

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] Re: TPP 7.0.0 Release is now available

Hello Juergen, Thank you for your question and use of TPP! Seq2MS's support in TPP is brand new. Truncation at the PTM usually indicates that the modification was not recognized or encoded in the model you applied. Can you tell me the model you applied and the modification you were searching?

[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] Hi I cannot access the gui anymore is there something I'm missing

Is this windows, linux, mac? Which version of the TPP software did you download and install? On Tue, Dec 5, 2023 at 11:35 AM Aarthie Senathirajah < animallover@gmail.com> wrote: > Hi David, > Thank you for your reply! > This is my OS 64-bit operating system, x64-based processor > But how do

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] running ASAPratio for SILAC data

ith me. >>>>> >>>>> Thanks! >>>>> -David >>>>> >>>>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar < >>>>> kumarsuders...@gmail.com> wrote: >>>>> >>>>>> *EXECUTING:

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

to say about this particular case in the next few days. >>> >>> Cheers! >>> -David >>> >>> On Nov 29, 2023, at 10:17 AM, sudarshan kumar >>> wrote: >>> >>> Hi David, >>> could you get time to see into my analysis? I need

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

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

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 10:35:06 AM UTC-7 David Shteynberg

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

Hi Murielle, Sorry this is a little confusing. Column "num unique peps" represents total number of unique peptides mapping to the protein. The "tot num peps" counts the PSMs that are "contributing evidence" (last column) to the protein, sometimes this number can be lower because not all

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

I am unable to reproduce this error when I download and run the tutorial on my windows or linux (ubuntu) machines with this tutorial data. Perhaps you can confirm that the fasta file you have is not getting corrupted somehow during your download or processing. Thanks. -David On Fri, Jun 10,

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

Which specific tutorial are you attempting so I can try to reproduce the issue? Thanks, -David On Fri, Jun 10, 2022 at 11:14 AM Malcolm Cook wrote: > Thank you. I concur deleting those characters resolves the issue. > > My colleague Gabriel actually was running the tutorial test. I will

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

Great! Thank you for keep and sharing your useful notes in this process. Let us know if you encounter other issues or have any questions. Cheers, David On Wed, Jun 8, 2022, 5:37 PM Malcolm Cook wrote: > Things I've tried and failed (with an `apachectl restart` after each) > >1. sudo chown

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

Great! Thank you. On Wed, Apr 6, 2022, 7:04 AM Shagun Gupta wrote: > Hi David > > Apologies, for some reason my post that it all worked out never made it > through. Instead one of my older replies I think got posted again. Sorry > for the confusion and thank you for your help! > > Shagun > >

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

Hello Shagun, Thank you for sharing your complete dataset. I still found the following in the conditions file you included: TMT10_VB297695_condition.xml This should be set to 0.001 for this analysis to work on your type of label. I am attaching the condition file with this change included

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

Hi Farshad, Thanks for providing your data and feedback so we can continue to improve our software. In this particular case, the mass values used by Tandem2XML were based on N14 and were likely to result in problematic pepXML representations of N15 data. I have added an option to Tandem2XML

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

Hello Shagun, Perhaps I am misunderstand here. As far as I know, TMT labels are isobaric and are quantified in the fragment ion spectra. Any peptide quantified would have to have the same precursor mass across all TMT labels. Presumably there are not that many peptides that are identical

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

Hello Shagun, I noticed in your condition file you are using TMT10 with the following masses: The difference between neighboring channels is <0.01 at the lowest and yet you are using tolerance of 0.2: I think the appropriate mass tolerance for

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. > > On Fri, Mar 25,

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

Please place your files on a shared drive and send me a link. On Fri, Mar 25, 2022 at 10:34 AM Shagun Gupta wrote: > Hi David > > Could you suggest a good email to reach you with? I can share the > pep.xml's and Libra condition file that way? > > -Shagun > > On Friday, March 25, 2022 at

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

Great thanks for finding the bug Will! The code will be part of the next release. On Sat, Sep 4, 2021 at 2:57 PM Will Comstock wrote: > 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

Re: [spctools-discuss] TPP 6.0 Libra Error

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

Re: [spctools-discuss] TPP 6.0 Libra Error

Hi Will, Thanks for sharing the dataset. I was able to reproduce the problem. When I have a potential solution I will let you know. Thank you for helping by reporting the error, it helps us improve the quality of the TPP over time. -David On Fri, Sep 3, 2021 at 9:34 AM Will Comstock wrote:

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?)

Will, Thanks for the update! Cheers, David On Thu, Apr 15, 2021, 6:22 AM Will Comstock wrote: > 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

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

Hi Oded, I think the old 5.2.0 might be under estimating the error rate as compared to the new release candidate. You cannot see the decoys here because of the settings you used. However your database has two independent sets of decoys available DECOY0 and DECOY1. Can you use one of the set

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

Dear Oded, Thanks for this. I ran a quick test and I actually observed a few more PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability cutoff for this dataset. Is the issue you see with PeptideProphet or iProphet results? Which spectra were getting excluded in the your

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

I don't mind taking a crack at it over vacation. Please let me know where I can pull the data from. I might not have quick solution for you but I can get started looking for the problem. Which search engine did you use here? I would need mzML data search results and the fasta database to get

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?)

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,

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

Hello again, I downloaded the code from sourceforge and replaced my version to test and at first it hung, like it did for you. I think this is because it wasn't installed by the installer. Here is how I got around the issue: 1. Open cmd prompt 2. Copy entire updatePaths.pl commandline

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

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 installer makes sure the permissions are setup correctly. Can you check the permissions for this file under properties -> security? On Tue, Mar 9, 2021,

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

;> You can compress the directory and post your dataset in the cloud and I >>>> will pull it down. Perhaps you can start with your search parameters. >>>> N15 labelling creates mass-shifts on every amino acid, how are you setting >>>> these? What PeptideProphet optio

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

to process? >> >> Thanks, >> -David >> >> >> On Tue, Feb 9, 2021 at 1:29 PM Asif Ahmed wrote: >> >>> Hi David, >>> >>> Thanks for your reply and appreciate your interpretation. >>> >>> How can i share the dat

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

This option changes the way mixture models in the TPP (PeptideProphet) are generated. The probabilities are estimated based on the mixture models learned by PeptideProphet. When the mixture models change so will the probabilities. On Wed, Jan 20, 2021 at 8:44 PM Soroush F wrote: > Dear David,

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

I am not sure I know a tool called "ProptideProphet" ;) Perhaps you tried to run PeptideProphet but it generated no results for you? When you run "Analyze Peptides" in the TPP interface, it should create a file called interact.pep.xml by default, that will contain probabilities among other

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

Hello again Emily, Apologies for the delay but I needed a bit more time to look into this. You are absolutely right about the titins causing this issue. The problem is the significant overlap in peptides in this very large titin group. Your database contains 343 variations of titin with

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

I just re extracted that file and I don't see the issue anymore. Perhaps this was a decompression issue. Thanks for checking. -David On Thu, Oct 22, 2020 at 12:19 PM Emily Kawaler wrote: > Hello, > Thanks so much for taking a look! I think the selenocysteines ("U") are > likely not the

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

Hi Emily, I analyzed the search results that you sent and I am seeing some strange things in at least one of the files you gave me. This may be causing some of the problems you saw. In file 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML on line 171821 there are some strange characters

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

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 On Sat, Oct 17, 2020 at 12:54 PM Emily Kawaler wrote: > I've uploaded the pepXML files, the parameters I used, and the database > here. >

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

Hello Alastair, Unless there is a mistake, I think the N15 mass string should be: -mA72.03415R160.10111N116.04293D116.02694C161.0307E130.04259Q130.05858G58.02146H140.05891I114.08406L114.08406K130.09496M132.04049F148.06841P 98.05276S88.03203T102.04768W188.07931Y164.06333V100.06841 See the

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

Hello Alastair, I downloaded the file you shared with me, however, there were no mzML files to match the pepXML files so I couldn't actually try the analysis. I will make another attempt if you can provide the mass spec data. Thanks, -David On Mon, Aug 17, 2020 at 11:21 AM 'Alastair

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

Hi Alastair, If your search results are either all heavy or all light (not variable mod searched) then you should also use option -S. 1). You cannot specify anything but single amino acids in this string. Your quantitation will be based on peptides without PTMs in this dataset. 2). -r8 is a

Re: [spctools-discuss] New to TPP: finding FDR corresponding to probability

Hello and welcome! You are correct! That is the model-estimated error/sensitivity table for ProteinProphet, in this case. A table of this sort is generated for PeptideProphet model estimates, iProphet based model estimates or ProteinProphet model estimates depending on the file being

Re: [spctools-discuss] New at TTP. Problem with PSM validation

Hi Carlos, The TPP is statistical software that takes advantage of statistical trends in data and requires many data points to work well. Do you have a dataset of reasonable size with maybe dozens or hundreds of spectra? Also can you post the file somewhere I can download it? Sending files as

Re: [spctools-discuss] New at TTP. Problem with PSM validation

Dear Carlos, There is probably some bug exposed by the modeling of this type of data with the specific set of options you enabled. If you are able to share a part of your dataset that can replicate the issue, I am able to troubleshoot this further. Thanks, David On Sat, Jul 18, 2020, 12:10

  1   2   >