[spctools-discuss] Automated TPP
Does anyone have a script that automatically runs the entire TPP process from converting .RAW files from the mass spectrometer to identify the proteins using protein prophet? I have used the TPP for a while and I don't like having to wait for each step to finish before I manually initiate the next step of the process. -- 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: Automated TPP
In Windows On Aug 3, 1:31 pm, Joseph Slagel joseph.sla...@systemsbiology.org wrote: Windows or Unix? A long time ago I played around with a Makefile that would run the process, and had the added benefit of knowing when to rerun certain parts when files changed (such as edits to parameters). -Joe On Wed, Aug 3, 2011 at 7:21 AM, John Bryant john_bryan...@yahoo.com wrote: Does anyone have a script that automatically runs the entire TPP process from converting .RAW files from the mass spectrometer to identify the proteins using protein prophet? I have used the TPP for a while and I don't like having to wait for each step to finish before I manually initiate the next step of the process. -- 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. -- 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: Automated TPP
In Windows 7 On Aug 3, 1:31 pm, Joseph Slagel joseph.sla...@systemsbiology.org wrote: Windows or Unix? A long time ago I played around with a Makefile that would run the process, and had the added benefit of knowing when to rerun certain parts when files changed (such as edits to parameters). -Joe On Wed, Aug 3, 2011 at 7:21 AM, John Bryant john_bryan...@yahoo.com wrote: Does anyone have a script that automatically runs the entire TPP process from converting .RAW files from the mass spectrometer to identify the proteins using protein prophet? I have used the TPP for a while and I don't like having to wait for each step to finish before I manually initiate the next step of the process. -- 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. -- 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: Automated TPP
I have a batch script which works pretty well, but continuously produces popup consoles while Sequest is running. Does anyone know a possible solution to this? ___ set /p filename= Please, type the name of your .RAW file (excluding the extension): set /p paramfile= Type the name of your parameter file (excluding the extension): ReAdW -v --mzXML %filename%.RAW runsearch -p%paramfile%.params -P15 %filename%.mzXML sequest -P%paramfile%.params -Dxargs out2XML.exe %filename% 1 -P%paramfile%.params -Etrypsin xinteract -N%filename%.pep.xml -p0.05 -l7 -O %filename%.pep.xml proteinprophet %filename%.pep.xml %filename%.prot.xml _ Adjust each line to specify where exactly your files are and save it as a batch script. As I said it works well, but it produces annoying popup as the Sequest search is running. -Ned On Aug 3, 2:38 pm, Joseph Slagel joseph.sla...@systemsbiology.org wrote: In theory it should work under nmake -- but I won't unleash this on anyone without extensively testing it first. Hopefully someone else has a solution, otherwise you could piece together a .bat file pretty easily by looking at the commands issued in petunia. -Joe On Wed, Aug 3, 2011 at 11:15 AM, John Bryant john_bryan...@yahoo.comwrote: In Windows 7 On Aug 3, 1:31 pm, Joseph Slagel joseph.sla...@systemsbiology.org wrote: Windows or Unix? A long time ago I played around with a Makefile that would run the process, and had the added benefit of knowing when to rerun certain parts when files changed (such as edits to parameters). -Joe On Wed, Aug 3, 2011 at 7:21 AM, John Bryant john_bryan...@yahoo.com wrote: Does anyone have a script that automatically runs the entire TPP process from converting .RAW files from the mass spectrometer to identify the proteins using protein prophet? I have used the TPP for a while and I don't like having to wait for each step to finish before I manually initiate the next step of the process. -- 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. -- 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. -- 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] how to merge sample in InterProphet
Hi, I have a data with 8 factions. I searched them in SEQUEST and X!tandem respectively. The output files after PeptideProphet are: Band1.sequest.pep.xml Band2.sequest.pep.xml Band3.sequest.pep.xml Band4.sequest.pep.xml Band5.sequest.pep.xml Band6.sequest.pep.xml Band7.sequest.pep.xml Band8.sequest.pep.xml Band1.xtandem.pep.xml Band2.xtandem.pep.xml Band3.xtandem.pep.xml Band4.xtandem.pep.xml Band5.xtandem.pep.xml Band6.xtandem.pep.xml Band7.xtandem.pep.xml Band8.xtandem.pep.xml How can I merge them in InterProphet? I asked this question in the workshop. I work on Linux. Could you write me an example of the command line that I should use? Yours, Kinfai -- 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.
Re: [spctools-discuss] how to merge sample in InterProphet
I would suggest you run these in separate directories maintaining the same basename of your spectrum files, this way iProphet will be able to recognized multiple searches of the same spectra. Run xinteract on each search combining all fractions from each search into a single analysis at the PeptideProphet level. Something like: cd sequest xinteract Band*.pep.xml cd xtandem xinteract Band*.pep.xml cd ../iprophet InterProphetParser ../sequest/interact.pep.xml ../xtandem/interact.pep.xml interact.iprophet.pep.xml Write back if you need further clarification. -David On Wed, Aug 3, 2011 at 3:06 PM, Kinfai Au kinfa...@gmail.com wrote: Hi, I have a data with 8 factions. I searched them in SEQUEST and X!tandem respectively. The output files after PeptideProphet are: Band1.sequest.pep.xml Band2.sequest.pep.xml Band3.sequest.pep.xml Band4.sequest.pep.xml Band5.sequest.pep.xml Band6.sequest.pep.xml Band7.sequest.pep.xml Band8.sequest.pep.xml Band1.xtandem.pep.xml Band2.xtandem.pep.xml Band3.xtandem.pep.xml Band4.xtandem.pep.xml Band5.xtandem.pep.xml Band6.xtandem.pep.xml Band7.xtandem.pep.xml Band8.xtandem.pep.xml How can I merge them in InterProphet? I asked this question in the workshop. I work on Linux. Could you write me an example of the command line that I should use? Yours, Kinfai -- 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. -- 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.
Re: [spctools-discuss] how to merge sample in InterProphet
Isn't the purpose of the base_name attribute in the pepXML to avoid the requirement of keeping the basename of the files the same? -Matt On 8/3/2011 5:32 PM, David Shteynberg wrote: I would suggest you run these in separate directories maintaining the same basename of your spectrum files, this way iProphet will be able to recognized multiple searches of the same spectra. Run xinteract on each search combining all fractions from each search into a single analysis at the PeptideProphet level. Something like: cd sequest xinteract Band*.pep.xml cd xtandem xinteract Band*.pep.xml cd ../iprophet InterProphetParser ../sequest/interact.pep.xml ../xtandem/interact.pep.xml interact.iprophet.pep.xml Write back if you need further clarification. -David On Wed, Aug 3, 2011 at 3:06 PM, Kinfai Aukinfa...@gmail.com wrote: Hi, I have a data with 8 factions. I searched them in SEQUEST and X!tandem respectively. The output files after PeptideProphet are: Band1.sequest.pep.xml Band2.sequest.pep.xml Band3.sequest.pep.xml Band4.sequest.pep.xml Band5.sequest.pep.xml Band6.sequest.pep.xml Band7.sequest.pep.xml Band8.sequest.pep.xml Band1.xtandem.pep.xml Band2.xtandem.pep.xml Band3.xtandem.pep.xml Band4.xtandem.pep.xml Band5.xtandem.pep.xml Band6.xtandem.pep.xml Band7.xtandem.pep.xml Band8.xtandem.pep.xml How can I merge them in InterProphet? I asked this question in the workshop. I work on Linux. Could you write me an example of the command line that I should use? Yours, Kinfai -- 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] XPRESS discrepancy between ProtXML and PepXML viewers and XPRESS viewer Options
Dear all, I am using TPP for SILAC analysis of Obritrap X!tandem data (with K+8/R +10). I noticed some differences between the peptide Xpress values shown thorough ProtXML viewer (XPressCGIProteinDisplayParser.cgi) and pepXML viewer (PepXMLViewer.cgi) and those that appear in XPressPeptideUpdateParser.cgi (which I assume are the correct ones). These differences are usually not that big (i.e 1-5%) in some cases can be totally off (i.e 0.1 vs 0.25). I have got similar outputs with TPP 4.4.1 on a Mac (OS 10.6) and Win XP. I should mention that I run it all through the gui. Any idea how to overcome it? Many thanks, Oded -- Forwarded message -- From: Jimmy Eng jke...@gmail.com Date: Dec 21 2010, 8:16 am Subject: XPRESS discrepancy between PepXML viewer and XPRESS viewer To: spctools-discuss Oliver, I finally had a chance to revert to 4.3.1 on two machines (linux windows desktop), runXPRESSon an old ICAT dataset, and view the ratios using new 4.4.1 XPressUpdateParser.cgi. On both systems I don't see the inconsistent ratios being reported for this dataset. Then I found some Orbi SILAC datasets which were run under 4.3.1. Viewing the ratios chromatograms using the current 4.4.1 cgi viewer shows the exact same ratios as calculated by 4.3.1XPRESS. At this point, I can't replicate the discrepancy you're seeing. My advice would be to run your analysis again and see if the discrepancy remains. If you still see the problem, isolate a small dataset (single lcms run) and send it to me (mzXML, pep.xml) along with yourXPRESSrun parameters. - Jimmy On Mon, Dec 13, 2010 at 10:02 AM, oschill...@gmail.com oschill...@gmail.com wrote: Sorry for my late reply: the discrepancy occurs when viewing a TPP 4.3 analysis with TPP 4.4. We have now rolled back to TPP 4.3 to keep our XPRESSanalysis consistent. Any advice on how to proceed in the future? Thanks Oliver On Nov 23, 5:46 pm, Jimmy Eng jke...@gmail.com wrote: Oliver, What parameters did you use to runXPRESS? The GUI showing elution profiles has no current support for the isotope option (summed intensities of first N isotope peaks) but otherwise should return the same ratios as that shown in the pepXML file. - Jimmy On Mon, Nov 22, 2010 at 5:09 AM, oschill...@gmail.com oschill...@gmail.com wrote: Dear TPP community, we notice a small discrepancy between theXPRESSvalues displayed in the PepXML viewer tab (table withpeptidesequences etc) and the XPRESStab (graphic display of elution peak). For almost all peptides, we observe slightly differentXPRESSvalues in both tabs. For example, apeptidehas anXPRESSvalue of 2.32:1 in the PepXML viewer and 2.27:1 in theXPRESSviewer. Our impression is that this discrepancy occurs as of TPP 4.4.1 and does not occur for TPP 4.3.x. Can anyone please advice us on how to proceed here? Thanks a lot Oliver -- 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 athttp://groups.google.com/group/spctools-discuss?hl=en. -- 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 athttp://groups.google.com/group/spctools-discuss?hl=en. -- 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.
