[spctools-discuss] Re: ProteinProphet

2008-10-16 Thread David Shteynberg
Hi Brian, It looks like you just committed a fix that changed the interactxsl file to interact.xsl. However, for consistency reasons shouldn't we be naming all peptide level results with a .pep. before the final extension. So instead of generating files interact.xsl and interact.shtml, these

[spctools-discuss] Re: no output when running ProteinProphet

2008-10-17 Thread David Shteynberg
It looks like PeptideProphet's quality check fail and throw out some potentially good models. Try rerunning the tool with the option to force the output of the models. On Fri, Oct 17, 2008 at 5:06 AM, John Lee [EMAIL PROTECTED] wrote: Anyone else met this problem?

[spctools-discuss] Re: InterProphetParser NSE model

2008-11-25 Thread David Shteynberg
Hi Dave, Thanks for your interest in iProphet. At some point I decided to disable the NSE model, since the way it was implemented it was semantically closer to Number of Sibling MS/MS Runs rather than Number of Sibling Experiments, and in that form it was not very effective and I decided to

[spctools-discuss] Re: TPP 4.1 - Peptide prophet

2008-12-08 Thread David Shteynberg
You might have to rerun the tool specifying a minimum probability of 0 (-p0 xinteract flag) On Mon, Dec 8, 2008 at 10:54 AM, Natalie Tasman [EMAIL PROTECTED] wrote: Hi Ian, Can you please tell us how many peptide IDs actually pass a probability cutoff of 0.05 or greater (by using the pepXML

[spctools-discuss] Re: Empirical Error Rate

2008-12-15 Thread David Shteynberg
Hi Dave, Yes there is such a tool and its integrated into the latest version of Petunia user interface. Are you using commandline based TPP or are you running Petunia? Thanks, -David On Mon, Dec 15, 2008 at 1:43 PM, Dave @ UPENN davejun...@gmail.com wrote: Good Evening, When a decoy

[spctools-discuss] Re: Reposting- I haven't gotten a response back yet to my PeptideProphetParser.exe error

2008-12-15 Thread David Shteynberg
Hi Amanda, The error message says: running: C:/Inetpub/tpp-bin/InteractParser interact.pep.xml c:/ Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/18337.pep.xml file 1: c:/Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/ 18337.pep.xml processed altogether 0 results This means there was a

[spctools-discuss] Re: XPRESS command failed

2009-01-15 Thread David Shteynberg
Before we can help you have to try to understand the nature of the message: XPRESS error - cannot open file from basename c:/Inetpub/wwwroot/ISB/data/testband4 This usually suggest a problem upstream of XPRESS. Can you verify that this file exists? Can you open your interact.pep.xml file in

[spctools-discuss] Re: XPRESS command failed

2009-01-15 Thread David Shteynberg
for Arg and 8.0 for Lys. We keep the default ratio option and unchecked all the remaining options. Thanks for your help. Camilo On Jan 15, 12:39 pm, David Shteynberg dshteynb...@systemsbiology.org wrote: Before we can help you have to try to understand the nature of the message: XPRESS error

[spctools-discuss] Re: ASAPRatio - multi-threading

2009-01-21 Thread David Shteynberg
Hi Brian, Yes, this would be a good optimization to make, but I think it would make sense to create an additional separate option for this. So in addition to having an option to compute the ratio from only the CID charge state, we would have an option to not try to compute the other ratios at

[spctools-discuss] Re: Reg:TPP combatibility with Shimadzu MALDI-TOF-TOF data

2009-02-17 Thread David Shteynberg
Hello Anand and Sergey, Negative values are placeholders to identify potentially correct PSMs when there is too little data, insufficient separation between positive and negative distributions in the model, or non-bimodal search results (often a result of bad search parameters missing static

[spctools-discuss] Re: Reg:TPP combatibility with Shimadzu MALDI-TOF-TOF data

2009-02-17 Thread David Shteynberg
17, 2:19 pm, David Shteynberg dshteynb...@systemsbiology.org wrote: Hello Anand and Sergey, Negative values are placeholders to identify potentially correct PSMs when there is too little data, insufficient separation between positive and negative distributions in the model, or non-bimodal

[spctools-discuss] Re: Reg:TPP combatibility with Shimadzu MALDI-TOF-TOF data

2009-02-17 Thread David Shteynberg
On Feb 17, 4:17 pm, David Shteynberg dshteynb...@systemsbiology.org wrote: PeptideProphet compute a probability that a PSM is correct GIVEN the data. So I am not sure I understand what you mean exactly when you say that this is mathematically wrong. It is not correct to compare

[spctools-discuss] Re: Reg:TPP combatibility with Shimadzu MALDI-TOF-TOF data

2009-02-17 Thread David Shteynberg
, David Shteynberg dshteynb...@systemsbiology.org wrote: I don't agree that any hidden links are introduced, rather some incorrect assumptions are exposed. When datasets are analyzed together this is very explicit. When you are expecting that these datasets should be independent but you

[spctools-discuss] Re: Way to access # corr and #incorr from Sensitivity/Error info from a script?

2009-03-02 Thread David Shteynberg
Hi Greg, This info is written at the top of the protXML file in tags: protein_summary_data_filter min_probability=0.00 sensitivity=1.000 false_positive_error_rate=0.464 predicted_num_correct=135 predicted_num_incorrect=117/ It should be straight forward to write a perl script with a regular

[spctools-discuss] Re: [PeptideProphet]How to define accurate mass

2009-03-03 Thread David Shteynberg
Hi Jun, You should use the accurate mass model when you are processing data from high-mass-accuracy instruments (e.g. Orbitrap and FT) and you are using monoisotopic precursor masses in your search params. -David On Mon, Mar 2, 2009 at 9:31 PM, jun junster@gmail.com wrote: Hi, everyone.

[spctools-discuss] Re: How to set PeptideProphet Options pane,Xpress Options pane and ASAPRatio Options pane for anaysis isotopic labeling data by O18

2009-03-06 Thread David Shteynberg
I the ASAPRatio pane select the labeled amino acids. For each labeled amino acids specify the total modified monoisotopic mass. You may want to narrow the m/z range if you have high-mass-accuracy data. -David On Thu, Mar 5, 2009 at 9:55 PM, hqzlul hqz...@gmail.com wrote: Hi everyone   I am

[spctools-discuss] Re: [PeptideProphet]How to define accurate mass

2009-03-17 Thread David Shteynberg
Yes. On Mon, Mar 16, 2009 at 11:59 PM, jun junster@gmail.com wrote: Hi, David well, I am using an LTQ Orbitrap instrument and set the precursor mass type to monoisotopic. And I was suggested by a technical support engineer from ThermoFisher that seeting the precursor tolerance to 50

[spctools-discuss] Re: decoy hit peptide probability from the semi-supervised mode peptideprophet

2009-03-17 Thread David Shteynberg
Hello Minyoung, In semi-supervised mode you give a decoy tag to PeptideProphet and you are telling the algorithm the known incorrect IDs. It is natural for the probabilities of the decoy sequences to then be assigned probabilities of zero. In xinteract there is an option to still compute the

[spctools-discuss] Re: iProphet

2009-05-13 Thread David Shteynberg
Hi Oded, Thanks for your interest in iProphet. When you use iProphet to combine the results of multiple search engines (although this is not a prerequisite for using iProphet), then iProphet will report the top scoring DB engine hit in the pepXML file for each spectrum searched. You will have a

[spctools-discuss] Letter of Support Request

2009-05-14 Thread David Shteynberg
Dear TPP Users, Last year many of you were kind enough to write excellent letters of support for our grant application to maintain funding for the Trans-Proteomic Pipeline. While this grant is still under review, we have been strongly encouraged to apply for funding for the TPP through the Grand

[spctools-discuss] Re: SILAC with ASAPratio

2009-05-19 Thread David Shteynberg
Hi Federico, Your parameter set looks correct. Have you tried to execute to program with this set of params? Did it seem to work? -David On Mon, May 18, 2009 at 6:32 AM, fto...@gmail.com fto...@gmail.com wrote: Hope not to be too annoying cause I am really enjoying this toolbox but I have

[spctools-discuss] Re: SILAC with ASAPratio

2009-05-22 Thread David Shteynberg
? On 20 Mag, 00:11, David Shteynberg dshteynb...@systemsbiology.org wrote: Hi Federico, Your parameter set looks correct.  Have you tried to execute to program with this set of params?  Did it seem to work? -David On Mon, May 18, 2009 at 6:32 AM, fto...@gmail.com fto...@gmail.com

[spctools-discuss] Re: problem with ASAPcgi display and iprophet

2009-05-27 Thread David Shteynberg
Hi Thomas, Because iProphet is so new not all of the links will work with it without some tweaks. Would you mind compressing the problem data and sending it to us through our FTP server so we can correct the broken links. Instructions for uploading data to our ftp server can be found on the

[spctools-discuss] Re: problem with ASAPcgi display and iprophet

2009-05-28 Thread David Shteynberg
Hi Brian, I don't have any problems with that change. Have you confirmed that it fixes the problem? Thanks, -David On Thu, May 28, 2009 at 9:15 AM, Brian Pratt brian.pr...@insilicos.com wrote: The problem, I think, is that interProphet is filtering out all analaysis_summary tags, when it

[spctools-discuss] Re: FDR Uncertainty Measures

2009-06-09 Thread David Shteynberg
Hi Dave, This is the basic standard error calculation that can be applied to a simple random sample. -David On Tue, Jun 9, 2009 at 6:43 AM, dctruddct...@ccmp.ox.ac.uk wrote: Hi, In the latest TPP versions ProphetModels.pl now calculates uncertainty values for the FDRs (both prophet and

[spctools-discuss] Re: quantification in ASAPRatio n-term labeled samples

2009-06-15 Thread David Shteynberg
Hello Filip, Xpress works using delta mass. Asap ratio on the other hand takes the mass of the modified form as input. If the dataset is high mass accuracy you also need to specify the monoisotopic masses of ALL your modifications even the ones not used for the label, unless you are doing

[spctools-discuss] Re: No peptide passing MPT filter

2009-06-18 Thread David Shteynberg
Hi Keren, You've managed to hit a bug in the current release that's been fixed in the upcoming release. To avoid this problem for now and to process your dataset you can disable the ACCMASS option which is causing the error, until the next release is available. I would also advise that you

[spctools-discuss] Re: No peptide passing MPT filter

2009-06-18 Thread David Shteynberg
Hi Keren, I forgot to mention that the error may also be getting caused by use of the NONPARAM (semi-parametric modelling option). Please disable this option for Mascot until the next release is available. Actually, either the ACCMASS or the NONPARAM could be causing your error message. Please

[spctools-discuss] Re: protXML question

2009-06-18 Thread David Shteynberg
Hello Andreas, Indistinguishable proteins must have all peptides in common (same peptide sequences and same number of enzymaticaly tolerable ends on the peptides). In a protein_group only some (not all) of the peptides will be shared by the proteins in the group. -David On Thu, Jun 18, 2009

[spctools-discuss] Re: combining X!Tandem / SEQUEST / MASQOT etc

2009-06-30 Thread David Shteynberg
Hi Christine, We do have a tool in the TPP, called iProphet, for combining search engines. This tool applies a set of 5 statistical models of which the search engine combining is merely one. We will have a paper coming out on iProphet in the near future. Meanwhile, the tool is available to

[spctools-discuss] Re: iProphet Information

2009-06-30 Thread David Shteynberg
Hi Jake, It is up to you to define the experiment boundaries. I would imagine that different fractions of SCX of a single sample, for instance, can be classified as one experiment. As long as different fractions or separate physical runs have different MS data file names there will be no

[spctools-discuss] Re: The problem with running xinteract on OMSSA pepxml

2009-07-02 Thread David Shteynberg
Hi Ping, The problem is this message: WARNING: No decoys with label DECOY were found in this dataset. reverting to fully unsupervised method. Iterations: .10.20 The OMSSA modelling relies on having a nonparameteric model which is built from decoys IDs from the database. Are you

[spctools-discuss] Re: Does Peptideprophet accept only a limited no. of pepXML files?

2009-07-02 Thread David Shteynberg
What was the problem with the final generated interact.pep.xml file? Can you verify that all of your pep.xml files are complete? Check their size and starting and ending tags for completeness. If there are any error message please post them here. -David On Thu, Jul 2, 2009 at 10:40 AM, Brian

[spctools-discuss] Re: The problem with running xinteract on OMSSA pepxml

2009-07-02 Thread David Shteynberg
If you are running the tpp on the commandline you can correct this problem in the omssa output by running the steps of xinteract separately and enabling InteractParser option -P. On 7/2/09, Jimmy Eng j...@systemsbiology.org wrote: Ping, I just downloaded OMSSA 2.1.4 and tried the direct

[spctools-discuss] Re: Spectra viewing problem

2009-07-06 Thread David Shteynberg
Hello Bernard, My best guess is that the '.' in your filename before the .mzXML is causing some parsing to break. Please change your file basename (everything before the extension) to include only alphanumeric characters and try again. Thanks, -David On Sat, Jul 4, 2009 at 10:20 AM,

[spctools-discuss] Re: trapper fails when large files processed

2009-07-07 Thread David Shteynberg
Hello Ilya, I have not used trapper but in a situation like this a more detailed description of the failure may be needed. Are there any error messages produced? What is the system you are running trapper on? What else have to tried to address this issue? Can you post a problem file to Tranche

[spctools-discuss] Re: iProphet Information

2009-07-13 Thread David Shteynberg
the same extensions and filenames (i.e. *.tandem.pep.xml - *.pep.xml    and   *.dat.pep.xml - *.pep.xml) for PeptideProphet to add the -E expt label? Bernt On Jul 1, 2:39 am, David Shteynberg dshteynb...@systemsbiology.org wrote: Hi Greg, TheiProphetpowerful tool that is very simple to run

[spctools-discuss] Re: The problem with running xinteract on OMSSA pepxml

2009-07-14 Thread David Shteynberg
Thanks for the fix. I already checked one in like it into SVN a few weeks back. The upcoming release will avoid this problem. -David On Tue, Jul 14, 2009 at 9:28 AM, Pingyanpp...@gmail.com wrote: Sure. I am not completely sure that my fix is correct. Under two functions:

[spctools-discuss] Re: trapper fails when large files processed

2009-07-20 Thread David Shteynberg
it. Thanks! On Jul 7, 8:16 pm, David Shteynberg dshteynb...@systemsbiology.org wrote: Hello Ilya, I have not used trapper but in a situation like this a more detailed description of the failure may be needed.  Are there any error messages produced? What is the system you are running trapper

[spctools-discuss] Re: xinteract returns 0 for all peptide prophet probabilities

2009-07-29 Thread David Shteynberg
Hello Scott, It sounds like the model PeptideProphet generates with the SVN version of the TPP fails the model quality controls on your data. I cannot be sure of the reason without seeing the data. Please post the file to our FTP site, instructions here:

[spctools-discuss] Re: xinteract returns 0 for all peptide prophet probabilities

2009-08-04 Thread David Shteynberg
Hi Scott, I just checked in a fix to this error in SVN. The problem was the spectrum names were getting extra whitespace at the end in the .tandem files, which were being propagated to the pepXML. The workaround that I committed trims any extra whitespace surrounding the spectrum name. The fix

[spctools-discuss] Re: problem for the tpp ananlysis with indexed database

2009-09-08 Thread David Shteynberg
Of David Shteynberg Sent: 04 September 2009 12:34 To: spctools-discuss@googlegroups.com Subject: [spctools-discuss] Re: problem for the tpp ananlysis with indexed database Hello Eileen, After you made the change to the sequest.params file you would need to reconvert your search results (out

[spctools-discuss] Re: problem for the tpp ananlysis with indexed database

2009-09-08 Thread David Shteynberg
-Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of David Shteynberg Sent: 04 September 2009 12:34 To: spctools-discuss@googlegroups.com Subject: [spctools-discuss] Re: problem for the tpp ananlysis with indexed database

[spctools-discuss] Re: Problems with TPP installation

2009-09-08 Thread David Shteynberg
Sounds like your apache webserver is not firing up correctly. Please check your apache weblogs for any clues. On Tue, Sep 8, 2009 at 3:49 AM, rhodearho...@gmail.com wrote: Dear friends, I am installing TPP. Unfortunately, after reboot, the check_env.pl reports as follows: --12:19:49--  

[spctools-discuss] Re: Problems with TPP installation

2009-09-08 Thread David Shteynberg
An other thing. Did you remember to install ActivePerl? This is free and required by the TPP. -David On Tue, Sep 8, 2009 at 12:06 PM, David Shteynbergdshteynb...@systemsbiology.org wrote: Sounds like your apache webserver is not firing up correctly.  Please check your apache weblogs for any

[spctools-discuss] Re: Problems with TPP installation

2009-09-09 Thread David Shteynberg
/Apache2.2/conf/extra/httpd-multilang-errordoc.conf preserved Successfully removed C:\Program Files\Apache Software Foundation\Apache2.2\conf\original\installwinconf.awk 2009/9/8 David Shteynberg dshteynb...@systemsbiology.org An other thing.  Did you remember to install ActivePerl?  This is free

[spctools-discuss] Re: Problems with TPP installation

2009-09-09 Thread David Shteynberg
What happens when you try to access simply http://localhost ? Thanks, -David On Tue, Sep 8, 2009 at 4:37 AM, rhodearho...@gmail.com wrote: Dear friends, I am installing TPP. Unfortunately, after reboot, the check_env.pl reports as follows: --12:19:49--  

[spctools-discuss] Re: Problems with TPP installation

2009-09-15 Thread David Shteynberg
is the proper alias path for tpp-bin, ISB, and schema? Second, are there any environmental path modifcations needed? Thanks, Mike On Sep 9, 6:14 pm, David Shteynberg dshteynb...@systemsbiology.org wrote: What happens when you try to access simplyhttp://localhost? Thanks, -David On Tue

[spctools-discuss] Re: Unknown error during iterations in PeptideProphetParser

2009-09-16 Thread David Shteynberg
Hello Melody, It appears you've discovered a bug in the code with this particular analysis. Would you please zip up the data directory (or just the analysis*.xml files) and post them to our ftp site, instructions here:

[spctools-discuss] Re: how is xtandem fval calcualted

2009-09-17 Thread David Shteynberg
The EXPECTSCORE option was something that was added after f-val at Alexey request. I believe the reason for the inclusion of this option is in the usage statement: E [only use Expect Score as the Discriminant(applies only to X!Tandem data, helpful for data with homologous top hits e.g.

[spctools-discuss] Re: exit code 35584 when running xinteract

2009-09-18 Thread David Shteynberg
Hi Andreas, I think you are doing everything correctly. The soruce of the problem is here: PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909181208 (linux)) akel...@isb read in 0 1+, 1135 2+, 137 3+, 18 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Iterations:

[spctools-discuss] Re: exit code 6400 when running xinteract on spectrast

2009-09-22 Thread David Shteynberg
This error can be safely ignored. It comes up because there is not decoy tag specified when ProtProphModel.pl runs. You are correct that this is no way to fail, this will be corrected in the future. Luis already pointed to the problem so this would be a quick fix. -David On Tue, Sep 22, 2009

[spctools-discuss] Re: tutorial for TPP on WIKI

2009-09-28 Thread David Shteynberg
Please see the tutorial at the following link: http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial -David On Mon, Sep 28, 2009 at 9:59 AM, dick rwin...@gmail.com wrote: Hi, I am trying to run the TransProteomePipeline tutorial on wikipedia but I cannot access the data.  Its

[spctools-discuss] Re: Analyzing filtered peptideprophet results in proteinprophet...

2009-10-19 Thread David Shteynberg
Hello Nick, You can run PeptideProphet once to find the probability threshold that satisfies your criteria. You can then rerun the pipeline, this time including ProteinProphet with the probability cutoff you decided on in the first pass. Hope that helps. -David On Mon, Oct 19, 2009 at 8:05

[spctools-discuss] Re: ASAPCGIDisplay.cgi error - OMSSA and iProphet .prot.xml

2009-10-29 Thread David Shteynberg
Hi Dave, This is not supported yet. Hopefully, this will become supported in the near future. Please send anymore issues you find like this here. Thanks, -David On Thu, Oct 29, 2009 at 3:01 AM, Dave Trudgian dct...@ccmp.ox.ac.uk wrote: Jake, Thanks for this, the CGI works for OMSSA

Re: [spctools-discuss] Re: base_name constraint in pepXML

2009-11-20 Thread David Shteynberg
Hi Hendrik, The element msms_pipeline_analysis/msms_run_summary has an attribute base_name to specify the path to the datafile. In case the searched file specified is different from the original data file there is another entry in the element

Re: [spctools-discuss] Re: base_name constraint in pepXML

2009-11-20 Thread David Shteynberg
OK I take that back. I see where the unique constraint is listed. I will have to consider your questions further. -David On Fri, Nov 20, 2009 at 10:27 AM, David Shteynberg dshteynb...@systemsbiology.org wrote: Hi Hendrik, The element msms_pipeline_analysis/msms_run_summary has an attribute

Re: [spctools-discuss] Re: base_name constraint in pepXML

2009-11-20 Thread David Shteynberg
. Let us know if you have other questions. -David On Fri, Nov 20, 2009 at 10:30 AM, David Shteynberg dshteynb...@systemsbiology.org wrote: OK I take that back.  I see where the unique constraint is listed.  I will have to consider your questions further. -David On Fri, Nov 20, 2009 at 10:27

Re: [spctools-discuss] Re: OMSSA files with PeptideProphet

2009-11-24 Thread David Shteynberg
wrote: David, Thanks Bill -Original Message- From: David Shteynberg [mailto:dshteynb...@systemsbiology.org] Sent: Monday, November 23, 2009 11:48 AM To: spctools-discuss@googlegroups.com Subject: Re: [spctools-discuss] Re: OMSSA files with PeptideProphet Hi Bill, Attached

Re: [spctools-discuss] Can PeptideProphet be used with any algorithm?

2009-12-01 Thread David Shteynberg
Hi, If your search algorithm or scoring can be reported in pepXML format we can extend the TPP quite easily to integrate your algorithm. Please send such a pepXML file and the search scores that are appropriate and we will work with you to resolve any pepXML issues you might have and retool the

Re: [spctools-discuss] error analyzing InSpecT results (pepxml) with PeptideProphet

2010-02-11 Thread David Shteynberg
Hi Christian, The problem is here: WARNING: Inspect only support semi-parametric PeptideProphet modelling, which relies on a DECOY search. You need to include Decoy sequences (with a decoy tag) in the protein database you are searching and specify this to PeptideProphet. If you are using

Re: [spctools-discuss] Peptide Probability Vs Peptide FDR (local)

2010-03-18 Thread David Shteynberg
Yes On Thu, Mar 18, 2010 at 3:13 PM, Minglism mingguo...@gmail.com wrote: Hello, I am trying to understand the different meaning (if any) between peptide probabilities assigned by peptideprophet and the concept of peptide local false discovery rate. I am not sure if I understand them

Re: [spctools-discuss] Re: PepXMLViewer - not well formed (invalid token) error

2010-03-31 Thread David Shteynberg
The problem could be caused by a bad character like appearing in one of your protein descriptions in the database and breaking the XML parsing. Can you search your fasta database for occurences of ? -David On Wed, Mar 31, 2010 at 1:33 PM, Brian Pratt brian.pr...@insilicos.com wrote: Huh,

Re: [spctools-discuss] protXML_v6?

2010-04-30 Thread David Shteynberg
Hi John, Yes you correct there are some changes to the format that have not been released in a new xsd yet. Thank you for identifying this issue. We will correct this in a future release. The confidence parameter is a measure similar to that described in States, D.J.et al (2006) Nature

Re: [spctools-discuss] Issue regarding TPP V4.3

2010-05-18 Thread David Shteynberg
It's is hard to say from your description exactly the problem with the analysis. The order of files given to xinteract should not affect results. Something is certainly not right in the analysis. If you post your files I can tell you more. -David On Tue, May 18, 2010 at 4:35 AM, lgillet

Re: [spctools-discuss] Re: Issue regarding TPP V4.3

2010-05-25 Thread David Shteynberg
Hi Ludovic, It seems the file you uploaded lgillet_pepxml_for_TPP4.3.rar is corrupted. At least I am unable to open it. Please upload again. Thanks, -David On Wed, May 19, 2010 at 2:54 AM, lgillet gil...@imsb.biol.ethz.ch wrote: Hi David, Hi Natalie, I just posted the 4 pepxml files which

Re: [spctools-discuss] Re: Issue regarding TPP V4.3

2010-05-26 Thread David Shteynberg
download, I can decompress it back). Thanks for having a look at this issue. Best, Ludovic On May 25, 7:24 pm, David Shteynberg dshteynb...@systemsbiology.org wrote: Hi Ludovic, It seems the file you uploaded lgillet_pepxml_for_TPP4.3.rar is corrupted.  At least I am unable to open it. Please

Re: [spctools-discuss] Re: Issue regarding TPP V4.3

2010-05-31 Thread David Shteynberg
:33 pm, David Shteynberg dshteynb...@systemsbiology.org wrote: Hi Ludovic, It is completely normal to expect some difference in the results between version of the software since the models maybe slightly different in new a version due to optimization, bug fixes and the sort.  Hopefully

Re: [spctools-discuss] Re: Issue regarding TPP V4.3

2010-06-02 Thread David Shteynberg
to a source where conditions such as not using a '.' character in the file's basename are described because i was not aware of that. many thanks in advance, andreas On Wed, Jun 2, 2010 at 12:17 AM, David Shteynberg dshteynb...@systemsbiology.org wrote: Hello Ludovic, I think the problem might

Re: [spctools-discuss] Re: Issue regarding TPP V4.3

2010-06-04 Thread David Shteynberg
too many people's work. Best (and respectful) regards, Ludovic On Jun 3, 12:52 am, David Shteynberg dshteynb...@systemsbiology.org wrote: Hi Andreas, I suspect this problem was only with your sequest search because of the offending spectrum I pointed out.  I've corrected the source

Re: [spctools-discuss] xinteract question

2010-06-09 Thread David Shteynberg
Hi Simon, This error indicates that the PepXMLViewer failed when it tried to index your pepxml file. .pepprophet.xml is not a normal extension produced by the TPP for a pepXML file. Can you describe exactly how you arrived at this pepXML file? Thanks, -David On Wed, Jun 9, 2010 at 1:46 AM,

Re: [spctools-discuss] prot.xml unreadable?

2010-06-22 Thread David Shteynberg
It looks like the failure is in the RT model. Please disable RT and try the analysis again. Thanks, -David On Tue, Jun 22, 2010 at 3:58 AM, KMackay skippymac...@googlemail.com wrote: Hi, I am getting an unreadable tag on the ProteinProphet results file and the file is not visible in the

Re: [spctools-discuss] Question on Mascot.dat file and database.fasta file

2010-06-28 Thread David Shteynberg
When charge states are not listed in the mzXML file you should run the command: MzXML2Search -mgf -c1-3 *.mzXML This will generate the mgf files to submit to Mascot. Once you get the .dat files back you should rename that to the original basename of the mzXML file with the .dat extension. Now

Re: [spctools-discuss] Question on Mascot.dat file and database.fasta file

2010-06-28 Thread David Shteynberg
at 5:24 PM, David Shteynberg dshteynb...@systemsbiology.org wrote: When charge states are not listed in the mzXML file you should run the command: MzXML2Search -mgf -c1-3 *.mzXML This will generate the mgf files to submit to Mascot. Once you get the .dat files back you should rename

Re: [spctools-discuss] TPP pipeline execution after the xtandem search results Total hits of 0

2010-07-01 Thread David Shteynberg
Hello Jagan, I am not sure what steps you took to do the search but I've tracked the problem down to windows style line ending characters '^M' ending up in the tandem xml file that I downloaded jagan-J134.xml. They present at the end of every spectrum name in the note label=Description tags.

Re: [spctools-discuss] OMSSA and TPP pipeline execution ...

2010-07-16 Thread David Shteynberg
, Jul 9, 2010 at 7:18 AM, David Shteynberg dshteynb...@systemsbiology.org wrote: Hi Jagan, It appears that the QC filters were triggered on the PeptideProphet MixtureModel.  This is likely due to too few data points in the analysis for good stats:  read in 0 1+, 82 2+, 44 3+, 0 4+, 0 5+, 0 6

Re: [spctools-discuss] OMSSA and TPP pipeline execution ...

2010-07-20 Thread David Shteynberg
? with regards, Jagan Kommineni On Sat, Jul 17, 2010 at 1:01 AM, David Shteynberg dshteynb...@systemsbiology.org wrote: Dear Jagan, The modelling for OMSSA (also Inspect and Myrimatch) is done with semi-parametric modeling which *requires* decoys to learn the shapes of the mixture model

Re: [spctools-discuss] protein prophet

2010-08-10 Thread David Shteynberg
This is important: cannot open DB C:\XCalibur\database\ipi_HUMAN_v3_74_withcontaminants_FRF Can you check if this files exists on your system? On Tue, Aug 10, 2010 at 2:24 AM, bio4647 bio4...@gmail.com wrote:  c:\Inetpub\tpp-bin\ProteinProphet c:/Inetpub/wwwroot/ISB/data/

Re: [spctools-discuss] RefreshParser error with Myrimatch

2010-08-11 Thread David Shteynberg
/ /sample_enzyme This search was configured to allow cleavage after protein N-terminal methionines, which unfortunately pepXML cannot represent properly. -Matt On 8/11/2010 10:35 AM, David Shteynberg wrote: Hi Ben, The latest version of myrimatch leaves out the sample enzyme flag that RefreshParser

Re: [spctools-discuss] segmentation fault error with iprophet of tpp 4.3.1

2010-08-24 Thread David Shteynberg
This version is old and contains many bug that have been fixed in the latest 4-4 version. Can you try that one? On Tue, Aug 24, 2010 at 2:01 PM, Andreas Quandt quandt.andr...@gmail.com wrote: dear list, for one of my data analysis with iprophet i get a segmentation fault error but i am not

Re: [spctools-discuss] PeptideProphet algorithm documentation?

2010-09-20 Thread David Shteynberg
Hi John, The target is for the quality of the software to improve with subsequent releases. Do you notice that you have more incorrect (decoy) hits with higher probability? BTW, the latest version is 4.4 not 4.3. For more information you can check the release notes

Re: [spctools-discuss] Re: PeptideProphet algorithm documentation?

2010-09-21 Thread David Shteynberg
not sure. To be clear, I'm not asking for full compliance with the literature, I just want to know if PeptideProphet differs from it. Thanks, John On Sep 20, 1:24 pm, David Shteynberg dshteynb...@systemsbiology.org wrote: Hi John, The target is for the quality of the software to improve

Re: [spctools-discuss] TPP 4.4 and Mascot

2010-09-23 Thread David Shteynberg
Hi Marco, I am not sure I follow exactly what you've done here. It doesn't appear that you are running ProteinProphet based on the steps you've outlined. I am not surprised the f-val histograms would look different between 2 and 3 since PeptideProphet applies an automatic probability filter of

Re: [spctools-discuss] Qualscore

2010-09-24 Thread David Shteynberg
Everything you need to run qualscore should be here: http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/qualscore/lib/ -David On Fri, Sep 24, 2010 at 12:08 PM, Vishal Swaroop vishal@gmail.com wrote: It is also important to know which version of JFreechart is used by qualscore. Quick

Re: [spctools-discuss] Re: Qualscore

2010-09-27 Thread David Shteynberg
Try here: http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/qualscore/ On Sat, Sep 25, 2010 at 5:22 AM, Bjorn caveman.bj...@gmail.com wrote: Hi, I would also like to try out qualscore, but I get the following error: Unable to access jarfile /usr/local/tpp/bin/qualscore.jar I looked in

Re: [spctools-discuss] Limit of iProphet

2010-09-29 Thread David Shteynberg
Hi Rachel, It is limited only by the amout of memory you have on your system. The memory req scales linearly with number of spectra being combined. Obviously the more spectra that are analysed together the better the statistics are going to be, but this too has a practical limit. Once you

Re: [spctools-discuss] Re: building ReAdW (fann.h?)

2010-10-12 Thread David Shteynberg
Yes, build quite nicely for me using gcc under linux and mingw. -David On Tue, Oct 12, 2010 at 10:57 AM, Jeffrey Milloy jeffrey.a.mil...@gmail.com wrote: Hi Brian Building is no longer essential for me, but I gave it a try anyways. the fann libraries are sorted out, but the gsl project is a

Re: [spctools-discuss] Running xinteract on Phenyx generated pepXML file gives error read no data

2010-11-08 Thread David Shteynberg
Phenyx search results can only be processed with the semi-parametric modeling based on decoys. Judging from name of your database, it does have decoys in there. Now you must tell PeptideProphet to use the semi-parametric model with xinteract option -OP and the decoy tag that all your decoy

Re: [spctools-discuss] Re: Running xinteract on Phenyx generated pepXML file gives error read no data

2010-11-09 Thread David Shteynberg
not worry about that? Thanks for your help. On Nov 9, 11:06 am, David Shteynberg dshteynb...@systemsbiology.org wrote: Phenyx search results can only be processed with the semi-parametric modeling based on decoys.  Judging from name of your database, it does have decoys in there.  Now you must

Re: [spctools-discuss] Re: Running xinteract on Phenyx generated pepXML file gives error read no data

2010-11-10 Thread David Shteynberg
6+, and 0 7+ spectra.  read in no data command /usr/local/tpp-4-4-0/bin/PeptideProphetParser 'interact.pep.xml' MINPROB=0 DECOYPROBS NONPARAM DECOY=decoy exited with non-zero exit code: 256 QUIT - the job is incomplete Thanks for your help Ira On Nov 10, 3:08 am, David Shteynberg

Re: [spctools-discuss] Re: Running xinteract on Phenyx generated pepXML file gives error read no data

2010-11-10 Thread David Shteynberg
as a separate step to map the IDed peptides to the proteins in the database. My code changes will be committed later today. -David On Wed, Nov 10, 2010 at 12:35 PM, David Shteynberg dshteynb...@systemsbiology.org wrote: Hi Ira, Thanks for providing your Phenyx search results.  I

Re: [spctools-discuss] why N-terminus protonated for dimethyl label on ASAPratio?

2011-01-11 Thread David Shteynberg
The total mass of the modified amino-acid / terminus is specified to ASAPRatio. The unmodified n-terminus of any peptide is 1.007825 (or the mass of H), since your termini are modified the mass of the modification will be added to 1.0078. Also, please update to the latest version of the TPP

Re: [spctools-discuss] Re: PepXMLViewer.cgi error on TPP4.4

2011-01-21 Thread David Shteynberg
You likely have no good hits in this dataset so the program assigns 0 probability. If you apply a probability filter of 0 instead of 0.05 (default) you will see all the spectra and the probability in the pepXML. -David On Thu, Jan 20, 2011 at 11:03 PM, furukie efur...@etc.a-star.edu.sg wrote:

Re: [spctools-discuss] processing crux/tide results with tpp

2011-02-02 Thread David Shteynberg
Your best bet is to try the code from trunk SVN. Have you tried it in NONPARAM mdoe? -David On Wed, Feb 2, 2011 at 12:52 PM, Andreas Quandt quandt.andr...@gmail.com wrote: hey jimmy and matt, i tried what jimmy suggested but are stuck again :-( i added the 'missing' scores as jimmy

Re: [spctools-discuss] processing crux/tide results with tpp

2011-02-02 Thread David Shteynberg
quandt.andr...@gmail.com wrote: hey david, thanks for answering! i used xinteract -dDECOY_ -OAdPlIw B08-02057_mod.pepXML to process the file. as you suggest using a trunk version: can you refer to a specific revision? cheers, andreas On Wed, Feb 2, 2011 at 9:57 PM, David Shteynberg dshteynb

Re: [spctools-discuss] PeptideProphet run failure ...

2011-02-07 Thread David Shteynberg
Hi Jagan, Thanks for the thorough bug report. Have you tried the latest version? The RT or PI models had bug that have been fixed since July. Also if you want to upload these search results I can try tracing the latest code on it. Cheers, -David On Sun, Feb 6, 2011 at 4:53 PM, Jagan

Re: [spctools-discuss] Re: PeptideProphet run failure ...

2011-02-08 Thread David Shteynberg
Best, John On Feb 8, 1:32 am, Jagan Kommineni jagan.kommin...@gmail.com wrote: David, I have updated our installation version of TPP with the latest version of the TPP. This bug has disappeared. Thanks for your suggestion. with regards, Jagan On Tue, Feb 8, 2011 at 6:06 AM, David

Re: [spctools-discuss] Re: ASAPRatio Display error from protXML Viewer ....

2011-02-15 Thread David Shteynberg
Hi Jagan, Yes, this is likely the source of the error. Thanks for tracking it down in the code. I will commit a fix to our svn repository. Thanks, -David On Mon, Feb 14, 2011 at 8:59 PM, Jagan Kommineni jagan.kommin...@gmail.comwrote: Dear All, Further investigation on this problem with

Re: [spctools-discuss] X!Tandem metabolic labeling with N15

2011-02-17 Thread David Shteynberg
ASAPRatio has supported N15 for awhile. It does require a really long commandline, see this thread: http://groups.google.com/group/spctools-discuss/browse_thread/thread/3be51d7bf8fa36cb/56c8d65c9105865d?lnk=gstq=15N+ASAPRatio+Jake#56c8d65c9105865d -David On Thu, Feb 17, 2011 at 12:26 PM, Jimmy

Re: [spctools-discuss] myrimatch and iprophet

2011-03-11 Thread David Shteynberg
Hi Matt, Is it possible to turn off the decoy altogether in the search when there are decoy in the database? I tried a search with DecoyPrefix = . Would that have the desired effect? Thanks, -David On Fri, Mar 11, 2011 at 6:52 AM, Matthew Chambers matt.chamber...@gmail.com wrote: 1. Yes. Set

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