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

[spctools-discuss] iprophet is search showing blank page

I have analyzed a data file using peptide prophet. I got results. But when I am analyzing by iprophet i see a blank page . can anyone tell me what does it mean. Where is the problem? Regards, Sudarshan -- You received this message because you are subscribed to the Google Groups

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hi Alejandro, I am trying (unsuccessfully) to replicate this behavior on a different iProphet combination of comet and xtandem results. Would it be possible for you to provide some test data so I can reproduce this specific bug in my environment? Thanks, -David On Thu, Jun 13, 2019 at 6:24 AM

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hi David, The test didn't went forward not because of TPP but because of how MSGF+ encodes the modifications. I have to troubleshoot that first. However, I don't know if that will make a big change. In TPP 5.1 and below I can do XPRESS quantitation when running iProphet of both results (Comet

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hi Alejandro, XPress might be getting confused with the way you've done the search. Can you redo the search once, using variable heavy label modification and see if it lets you quantify the results? Thanks, -David On Tue, Jun 11, 2019 at 9:53 AM Alejandro wrote: > Hi David, > > No, I

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hi David, No, I haven't moved the files. I grep mzML and it has 4 instances, one for Heavy, one for Light for Comet, as well as one Heavy and one Light for MSGF. Running each independently (Comet or MSGF+) generates no error. Thanks, Alejandro On Tuesday, June 11, 2019 at 4:27:28 PM UTC+2,

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hi Alejandro, It appears that XPress runs for awhile then crashes in the middle of the file. This may indicate that different ms run in the pepxml file reference different mzML files to extract the data, and some of those mzML references could be incorrect. Have you moved the files around after

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hi David, I re-mapped it and now is working. A step forward. Now, I'm running XPRESS and I get an error when running it within iProphet, I use: /usr/local/tpp/bin/XPressPeptideParser interact.ipro.pep.xml -m10 -a -c5 -H -b -i -nn,6.031817 -nK,6.031817 And get always: *EXECUTING: cd

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hello Alejandro, This is a new issue so that's good, as we have made some progress. I am not sure why ProteinProphet is telling you you have two different databases referenced by your two searches. Can you either post your pep.xml input file and database for me to test with ProteinProphet or

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

HI David, Sorry for the late reply, I was out of town. Thanks for looking into it. I recompiled and installed the revision 7932. It now runs iProphet with those files! However, ProteinProphet now fails with the following error: COMMAND 1 [MON JUN 10 18:28:57 2019]show *EXECUTING: cd

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hello Alejandro, I have committed a fix for this problem. Would you mind seeing if it works on your end? The revision number is 7932. Thanks for reporting the issue and helping to make the TPP better. Cheers, -David On Mon, Jun 3, 2019 at 1:45 AM Alejandro wrote: > Hi David, > > I

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

I was able to replicate the error on a different dataset. I will work on a solution in the coming days, meanwhile the older version of iProphet will work just fine. The new version will be faster when it's released but results shouldn't change. Cheers, David On Mon, Jun 3, 2019, 4:45 AM

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Apologies for the misspellings in my last message...I am typing this on my phone On Mon, Jun 3, 2019, 9:20 AM David Shteynberg < david.shteynb...@systemsbiology.org> wrote: > Can ypu post your msgf and comet results for me to download and test. > Please let me know. Also if you are at ASMS,

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Can ypu post your msgf and comet results for me to download and test. Please let me know. Also if you are at ASMS, stip by our booth and I can get your dataset to test there. Cheers, David On Mon, Jun 3, 2019, 4:45 AM Alejandro wrote: > Hi David, > > I installed the revision 7931 and it gives

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hi David, I installed the revision 7931 and it gives the same error: Running FPKM NSS NRS NSE NSI NSM NSP Model EM: Computing NSS values ... Creating 1 threads Wait for threads to finish ... done Computing NRS values ... Creating 1 threads Wait for threads to finish ...

Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hello Alejandro, It appears that you are coming across an iProphet error in that svn code revision. Are you willing to test if the latest revision (7931) fails in the same way on your data? Otherwise, if you are able to share the data I can attempt to replicate the error myself and correct the

[spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04

Hello all, I'm having trouble running TPP 5.2 in general in Ubuntu 18.04. I followed the compilation guideline, and after using svn checkout -r 7922 (as recommended by Eric) it went ahead, although I still have some things that are broken, like checking for the ions in the pepxml file. I get

Re: [spctools-discuss] iProphet for Leucine/isoleucine IDs

Yes your understanding of the issue is spot on. iProphet converts everything to L for comparison, then reports the top hit from the highest scoring search engine as reported by the search engine. Post processing has to take care of how to treat the variants. Cheers, -David On Tue, Jun 12, 2018

Re: [spctools-discuss] iProphet for Leucine/isoleucine IDs

Hi David, Thank you for the quick reply. The three search engines I am using they rank I/L variant peptides inconsistently. Some ranks Leucine-version as rank 1, some ranks Isoleucine-version as rank 1. Then in iProphet pepXML file I observed that for each spectrum iProphet picks rank 1 hit info

Re: [spctools-discuss] iProphet for Leucine/isoleucine IDs

Hello Chih-Chiang, iProphet will convert all Isoleucines reported to Leucines for comparison purposes. Have you observed an error in your analyses? -David On Tue, Jun 12, 2018 at 9:06 AM, Chih-Chiang Tsou wrote: > Dear TPP developers, > > I have a question regarding how iProphet handles

[spctools-discuss] iProphet for Leucine/isoleucine IDs

Dear TPP developers, I have a question regarding how iProphet handles ambiguous I/L IDs from different search engine. I am using X!Tandem, Comet, and MSGF+ and combine the results using iProphet, and noticed that the three search engines have different rules ranking I/L hits. So how does

Re: [spctools-discuss] iProphet command failure (file not found: not created or deleted?) with interact.pep.xml file from MSFragger result

Thank you for following up. On Oct 23, 2017 8:34 PM, "Adam R" wrote: > Hi David, > > Just wanted to confirm that I had success with the patch that you > provided. Thanks again! > > Best, > > Adam > > > On Monday, October 23, 2017 at 4:35:20 PM UTC-5, David Shteynberg wrote:

Re: [spctools-discuss] iProphet command failure (file not found: not created or deleted?) with interact.pep.xml file from MSFragger result

Hi David, Just wanted to confirm that I had success with the patch that you provided. Thanks again! Best, Adam On Monday, October 23, 2017 at 4:35:20 PM UTC-5, David Shteynberg wrote: > > Hi Adam, > > Thanks for submitting the bug report. I have traced it to a problem with > iProphet

Re: [spctools-discuss] iProphet command failure (file not found: not created or deleted?) with interact.pep.xml file from MSFragger result

Thanks David! -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to

Re: [spctools-discuss] iProphet command failure (file not found: not created or deleted?) with interact.pep.xml file from MSFragger result

Hi Adam, Thanks for submitting the bug report. I have traced it to a problem with iProphet processing small files. I have corrected the issue and have a patch here: https://www.dropbox.com/s/mq9yv5a4ew9umhe/InterProphetParser.exe?dl=0 Please replace your existing copy in

Re: [spctools-discuss] iProphet command failure (file not found: not created or deleted?) with interact.pep.xml file from MSFragger result

I have run the TPP on MSFragger results, including iProphet, before. What parameters did you use for PeptideProphet? What was the output of that command? Is it possible that you don't have any high scoring PSM left after PeptideProphet filtering? Thanks, -David On Mon, Oct 23, 2017 at 11:42

[spctools-discuss] iProphet command failure (file not found: not created or deleted?) with interact.pep.xml file from MSFragger result

Hi Everyone, I am running into a problem with iProphet when trying to perform additional validation on PeptideProphet files sourced from MSFragger pep.xml output. The command fails and shows the warning "file not found: not created or deleted?" Has anyone else had this issue before? I would

Re: [spctools-discuss] iProphet process

Hi Yaarub, When you combine the results of multiple searches in iProphet each search must first be analyzed independently using PeptideProphet. Then the PeptideProphet results (interact.pep.xml by default) from each of the search engines must be input to iProphet on the refine/combine analysis

[spctools-discuss] iProphet process

Hello Everyone, I have an issue with iProphet and I would be grateful if someone could help as I am new to TPP. I am trying running both tandem and comet search engine using QExactive Plus-acquired data and but I have been facing an issue with iProphet as the process fails. I have

Re: [spctools-discuss] iProphet mistakenly parses FPKM values when using a NextProt peff database (TPP v. 5.0)

I can't find the string "FPKM=" anywhere in the database, so perhaps it's an erroneous message. My version is TPP v5.0.0a5 downloaded on 3/10/2016 On Mon, Apr 4, 2016 at 10:39 AM, David Shteynberg < david.shteynb...@systemsbiology.org> wrote: > Hello Jason, > > In an earlier version of iProphet

Re: [spctools-discuss] iProphet mistakenly parses FPKM values when using a NextProt peff database (TPP v. 5.0)

Hello Jason, In an earlier version of iProphet FPKM message was being printed erroneously. Does the peff database actually contain "FPKM=" in the description? If the FPKM model was actually used you would have an FPKM model reported in the pepXML file and the models viewer should display it.

[spctools-discuss] iProphet mistakenly parses FPKM values when using a NextProt peff database (TPP v. 5.0)

I've done several searches using the nextprot_all peff database from ftp://ftp.nextprot.org/pub/current_release/peff/ At the iProphet step I see the message that the FPKM model is being activated: FPKM values are available, to disable rerun with option NOFPKM ... This is probably due to the

[spctools-discuss] iProphet analysis: cannot see the iprob model

Dear all, I'm running TPP v.4.4 rev 1, on W7 with Apache HTTP server 2.2 and ActivePearl 5.8.9 (I'm a biologist so please forgive me if I write any mistake about informatics/programming). I've got 2 biological replicates of my experiments, each experiment include 13 fractions. I've also got 2

Re: [spctools-discuss] iProphet pepXML Lacks Good File Count

Hi Brendan, I considered this option but it is not so easy to do with iProphet drawing the results for one search run from multiple possible search engines a single MS runs spectra may now be reported across several msms_run_summary elements. Computing how many will be reported is possible, and

[spctools-discuss] iProphet pepXML Lacks Good File Count

The BiblioSpec library builder builds spectral libraries from many peptide search formats. It has long supported pepXML from PeptideProphet. I am now looking at expanding this support to include pepXML from iProphet. One issue I have encountered, however, is that unlike the PeptideProphet

[spctools-discuss] iProphet probability

Dear all In my iProphet output I get for each spectrum a separate iProphet probability and I was wondering why, because in the iProphet paper it says that as the main outcome, iProphet permits the calculation of more accurate posterior probabilities and FDR estimates at the level of unique

Re: [spctools-discuss] iProphet probability

Hi Olga, While the best iProphet probability is saved per spectrum (also the PeptideProphet probability) in the case of multiple searches this is done for completeness of the pepxml file. We want to show you the best ID for each spectrum you search. However, when ProteinProphet runs in IPROPHET

[spctools-discuss] iProphet performance

Hi, We've been using iProphet (4.4 Vuvuzuella) and noticed the following: 1) It seems to crash when we have a decent number of pep.xml files (e.g., around 50) from pepXML feeding it. Based on past posts as well as our own monitoring of the memory, it probably just ended up using too much memory

[spctools-discuss] iProphet + ProteinProphet: a bug or just me not doing it right?

Hello, First: I'm using TPP 4.4 rev 1 on Mac OS 10.6.8 Let me describe the situation: - I merge my tandem.pep.xml files in the xinteract GUI. - I select decoy option with decoy tag. - I select the run iProphet box and just below I select the run ProteinProphet on these results box. - run. The

[spctools-discuss] iprophet error

unknown error run_in c:/Inetpub/wwwroot/ISB/data/iprophet_test; c:\Inetpub\tpp-bin \InterProphetParser c:/Inetpub/wwwroot/ISB/data/iprophet_test/ Dta_Out.pep.xml interact.iproph.pep.xml command

[spctools-discuss] iProphet Information

I was wondering if someone could post some more detail on iProphet. One thing that I would like to know is what all command line arguments it takes, maybe some sample command lines, as that is how I work with the TPP tools. I've gotten a little behind on some of the newer tools, but I think

[spctools-discuss] iProphet

Hi all, Is there a way to display Mascot or/and X!tandem search scores (ion score/expect) in iProphet.pep.xml? I'm using TPP v4.3 JETSTREAM (unstable dev prerelease) rev 0 on Mac Os X but had the same issue with TPP 4.2.0 on WinXP. In addition what is the proper reference for citing iProphet (if

[spctools-discuss] iPROPHET

Hi all, I am trying to run iPROPHET within the latest version of TPP (4.1.1) and got a little confused with the pipeline. I will try to elaborate a few questions and would appreciate any help. 1) I 've been using TPP for a few months now and my understanding is that I should run iProphet in the