[spctools-discuss] Re: Error using mzXML.gz as input
Hi Brian, Thanks for the quick reply - this fix does solve the search results file name issue but now there are problems with viewing the spectra (using pepXML viewer) which lead to Windows error message saying: plot-msms.cgi has encountered a problem and needs to close. We are sorry for the inconvenience. etc. In the Apache error log I case see the following line if that might help somehow: [Tue Mar 03 11:16:28 2009] [error] [client 127.0.0.1] Use of uninitialized value in -d at C:/Perl/lib/CGI.pm line 4083., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=displaypage=results [Tue Mar 03 11:16:52 2009] [error] [client 127.0.0.1] Premature end of script headers: plot-msms.cgi, referer: http://localhost/ISB/data/OK1/June07/interact.pep.shtml Cheers, Oded On Mar 2, 9:43 pm, Brian Pratt brian.pr...@insilicos.com wrote: Oded, I'm sure you're right in your diagnosis, and thanks for doing the hard part! Try changing this line $out_file =~ s/\.mz[X]?ML$/\.tandem/i; to $out_file =~ s/\.mz[X]?ML(\.gz)?$/\.tandem/i; Please let me know if that works and I'll make the change for the next release. Thanks, Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Oded Sent: Saturday, February 28, 2009 11:33 AM To: spctools-discuss Subject: [spctools-discuss] Error using mzXML.gz as input Hi all, I'm having problems using the gzipped mzXML files as input (In TPP 4.2 both on OS X and Win). While doing X!Tandem search the results file overwrite the input file and appear under that same name without the .tandem For example the search results of Seq1.mzXML.gz will have the name of Seq1.mzXML.gz and not the name Seq1.tandem or something similar. (look like similar to what happened in 4.1 rev while using mzXL see:http://groups.google.com/group/spctools-discuss/browse_thread/thread/63b 8a308c04aaf3d/1cadb91f3ac730b5?lnk=gstq=mzml#1cadb91f3ac730b5 so I guess it shouldn't be too hard to fix) Cheers, Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Error using mzXML.gz as input
Hi Oded, If you'll put the offending file on ftp://insilicos.serveftp.net/pub I'll see what I can find out. Thanks, Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Oded Sent: Tuesday, March 03, 2009 1:25 AM To: spctools-discuss Subject: [spctools-discuss] Re: Error using mzXML.gz as input Hi Brian, Thanks for the quick reply - this fix does solve the search results file name issue but now there are problems with viewing the spectra (using pepXML viewer) which lead to Windows error message saying: plot-msms.cgi has encountered a problem and needs to close. We are sorry for the inconvenience. etc. In the Apache error log I case see the following line if that might help somehow: [Tue Mar 03 11:16:28 2009] [error] [client 127.0.0.1] Use of uninitialized value in -d at C:/Perl/lib/CGI.pm line 4083., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=displaypage=results [Tue Mar 03 11:16:52 2009] [error] [client 127.0.0.1] Premature end of script headers: plot-msms.cgi, referer: http://localhost/ISB/data/OK1/June07/interact.pep.shtml Cheers, Oded On Mar 2, 9:43 pm, Brian Pratt brian.pr...@insilicos.com wrote: Oded, I'm sure you're right in your diagnosis, and thanks for doing the hard part! Try changing this line $out_file =~ s/\.mz[X]?ML$/\.tandem/i; to $out_file =~ s/\.mz[X]?ML(\.gz)?$/\.tandem/i; Please let me know if that works and I'll make the change for the next release. Thanks, Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Oded Sent: Saturday, February 28, 2009 11:33 AM To: spctools-discuss Subject: [spctools-discuss] Error using mzXML.gz as input Hi all, I'm having problems using the gzipped mzXML files as input (In TPP 4.2 both on OS X and Win). While doing X!Tandem search the results file overwrite the input file and appear under that same name without the .tandem For example the search results of Seq1.mzXML.gz will have the name of Seq1.mzXML.gz and not the name Seq1.tandem or something similar. (look like similar to what happened in 4.1 rev while using mzXL see:http://groups.google.com/group/spctools-discuss/browse_thread/thread/63b 8a308c04aaf3d/1cadb91f3ac730b5?lnk=gstq=mzml#1cadb91f3ac730b5 so I guess it shouldn't be too hard to fix) Cheers, Oded --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: [PeptideProphet]How to define accurate mass
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. i'm a rookie user of TPP tools through network browser interface. the instrument i am using is an LTQ orbitrap. when I came to the analyze peptide step, I got confused with the PeptideProphet option Use accurate mass binning. I think it can be enabled when using very small precursor tolerance, such as 5 ppm. But the protrocol i follow is set precuesor tolerance to 50 ppm and set the filter to 5 ppm through Bioworks interface. Can I enable the use accurate mass binning using the tolerance of 50 ppm?? i appraciate your answers! --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
