Re: [spctools-discuss] Index mzXML file error
Hi Luis, Thank you for your answer. Pavel -- 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 spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Index mzXML file error
Hi, I try to re-index some mzXML files (SWATH wiff files converted to mzML with AB Sciex convertor and then using MSConvert for mzML to mzXML conversion) with TPP, but the new files are not created. The error below still occurs. Any idea? Thanks COMMAND 1 [SAT MAR 17 16:42:17 2018] EXECUTING: C:/TPP/bin/indexmzXML d:/TPP/data/1.mzXML indexmzXML Analyzing: d:/TPP/data/1.mzXML Validate index: d:/TPP/data/1.mzXML Command Successful RETURN CODE:0 COMMAND 2 [SAT MAR 17 16:42:22 2018] EXECUTING: mv -v d:/TPP/data/1.mzXML d:/TPP/data/1.old_index.mzXML d:/TPP/data/1.mzXML -> d:/TPP/data/1.old_index.mzXML Command Successful RETURN CODE:0 COMMAND 3 [SAT MAR 17 16:42:22 2018] EXECUTING: mv -v d:/TPP/data/1.mzXML.new d:/TPP/data/1.mzXML mv: d:/TPP/data/1.mzXML.new: No such file or directory Command FAILED RETURN CODE:256 -- 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 spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
Re: [spctools-discuss] protein identification FDR
Hi Jesse, thank you for your answer. I am interested in protein identification (for now) so it means that I have to estimate FDR for proteins only. I was just confused because of different information in different papers, now it's clear (I'd better ask now before presenting results). Thanks again, Pavel -- 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 spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[spctools-discuss] protein identification FDR
Hi all, I have a question about FDR estimation for protein identification (using reversed decoy database together with target database in a single file). I can estimate the probability threshold for peptides to get for example 1% FDR. My question is how to use this peptide probability threshold for protein identification? Do I have to filter out peptides below the probability threshold before ProteinProphet analysis(how?)? Or do I have to run ProteinProphet, then filter out peptides below the threshold and then estimate FDR for proteins? Or just etimate FDR on the protein level? What is the right way ? This is probably a silly question but I am confused about information I found in different papers, sometimes there are FDR estimations on the protein level only, sometimes there are FDR for peptides only and sometimes one can found info like „FDRs for both peptides and proteins were x%“. Thank you Pavel -- 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 spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[spctools-discuss] Re: Replicate data processing
Hi Jason, Thank you for your answer. I just want to assure myself - is it possible to do this like selecting two or more files (pep.xml after a tandem search) in TPP with the selection of one interact.pep.xml output file? Since I use the Windows TPP this would be the best way if it is ok. I appreciate your help, thanks. Pavel the procedure you wrote the same Dne pátek, 1. března 2013 17:51:05 UTC+1 Jason Winget napsal(a): Hi Pavel, I believe that the way to merge data is as follows: 1. Merge the pep.xml results (from a single search engine) using InteractParser into an interact.pep.xml 2. Run RefreshParser on the interact.pep.xml 3. Continue the TPP pipeline (PeptideProphet, iProphet, ProteinProphet) on the interact.pep.xml This should work for either technical replicates or fractionated samples. Alternatively I believe the xinteract command will handle a lot of this for you. Run xinteract (from the command line) without arguments for a comprehensive usage statement. You can also get more information here: http://tools.proteomecenter.org/wiki/index.php?title=TPP:Developer_Documentation#Running_the_TPP Best, Jason On Thursday, February 28, 2013 1:26:18 PM UTC-8, Pavel wrote: Dear all, I would like to ask a couple of questions about replicate data processing. I appreciate any comments on this topic. 1. What is the best step to „merge data“ for technical replicates in TPP? For example, I have 5 runs of the same sample (to identify as much proteins/peptides as possible) and searched each file against database. Do I have to select all the files for PeptideProphet analysis and thus merge them to one pep.xml file? Or do I have to analyse each file separately and select the five pep.xml files in ProteinProphet with exporting to one prot.xml file? I tried both the ways and the results differed just a bit (only probability values, not proteins identified) which I guess is due to the different number of spectra/peptides used in the analysis. I just wonder what is the best way from the statistical point of view. 2. The same question as above but when one deals with fractions of the same sample (e.g., SCX fractions). What is the step in TPP to „merge data“? 3. And what about the combination of fractions and technical replicates? Thanks for your comments, Pavel PS: I would like to thank the authors of TPP, I have finally installed it and have to say it is an amazing software. -- 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 spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [spctools-discuss] Installation problem (perl?) - tpp 4.6.1
Hi All, Finally, I decided to install TPP on another PC - there was no internet connection and possible problems with upgrade to a newer version of Perl so this is the easiest way. If anyone has the same problem, the solution is as describe above (installation of missing perl modules) - hope it helps someone. -- 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 spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [spctools-discuss] Installation problem (perl?) - tpp 4.6.1
Hi VaI, Thank you for your answer. I checked the file and it is identical. So I think the problem is Perl. Pavel -- 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 spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [spctools-discuss] Installation problem (perl?) - tpp 4.6.1
Hi Joe, Thank you for the answer. I looked for the module in Perl manager and it is missing, so this is apparently the problem. I found the right module(s) but it is not possible to install them directly using PPM. As I am not into IT, I am struggling to find information how to install it - I will have to call someone familiar with this kind of stuff probably :) Thanks again and I will let you know whether it helps or not. Pavel -- 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 spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[spctools-discuss] Installation problem (perl?) - tpp 4.6.1
Dear All, I would like to ask you for your help. I installed TPP v4.6.1 (windows version) with Apache (port 8080), everything seems to be OK - when I try localhost:8080 I can see It works. However, it is not possible to run TPP, I can see only the Internal server error page. I think the problem is in Perl according to the Apache error log: [Tue Feb 12 11:51:42 2013] [error] [client 127.0.0.1] Premature end of script headers: tpp_gui.pl [Tue Feb 12 11:51:42 2013] [error] [client 127.0.0.1] Can't locate IO/ Compress/Zip.pm in @INC (@INC contains: C:/Perl/site/lib C:/Perl/ lib .) at C:\\Inetpub\\tpp-bin\\tpp_gui.pl line 16. [Tue Feb 12 11:51:42 2013] [error] [client 127.0.0.1] BEGIN failed-- compilation aborted at C:\\Inetpub\\tpp-bin\\tpp_gui.pl line 16. I spent a couple of days searching this group for a solution but I have no clue what to do... I guess Perl (5.8.8 b820) is the problem, I did not try to re-install(?) it yet as I run Mascot on this PC and do not want to disrupt it (I am not into IT :) Any help would be appreciated. Thank you Pavel -- 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 spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
