[spctools-discuss] spectrast consensus RTs
Hi all, After creating a SpectraST consensus library the .sptxt file always contains three retention times per peptide entry (something like 'RetentionTime=6045.8,6061.1,6032.5'). Additionally, I've tried creating a best replicate library and there still always three entries in the RetentionTime. Does anybody know what these three values represent and/or how they are calculated? I can't find this described in the documentation. Many thanks for any assistance. Best, Ben -- 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] spectrast consensus RTs
Hi Ben, they are average,max,min among the replicates. Eric -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools- disc...@googlegroups.com] On Behalf Of Ben Collins Sent: Thursday, February 02, 2012 1:59 AM To: spctools-discuss Subject: [spctools-discuss] spectrast consensus RTs Hi all, After creating a SpectraST consensus library the .sptxt file always contains three retention times per peptide entry (something like 'RetentionTime=6045.8,6061.1,6032.5'). Additionally, I've tried creating a best replicate library and there still always three entries in the RetentionTime. Does anybody know what these three values represent and/or how they are calculated? I can't find this described in the documentation. Many thanks for any assistance. Best, Ben -- 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] spectrast consensus RTs
Great! Thanks Eric. On Feb 2, 2012 4:02 PM, Eric Deutsch edeut...@systemsbiology.org wrote: Hi Ben, they are average,max,min among the replicates. Eric -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools- disc...@googlegroups.com] On Behalf Of Ben Collins Sent: Thursday, February 02, 2012 1:59 AM To: spctools-discuss Subject: [spctools-discuss] spectrast consensus RTs Hi all, After creating a SpectraST consensus library the .sptxt file always contains three retention times per peptide entry (something like 'RetentionTime=6045.8,6061.1,6032.5'). Additionally, I've tried creating a best replicate library and there still always three entries in the RetentionTime. Does anybody know what these three values represent and/or how they are calculated? I can't find this described in the documentation. Many thanks for any assistance. Best, Ben -- 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] Re: Help please: having trouble converting Waters MRM raw data to mzXML
Hello Matt, Thanks for the comments. I tried converting the raw data to mzML instead of mzXML as well. It didn't work. All I got in the mzML file is the column heads, but no content. Harry On Feb 1, 1:40 pm, Matthew Chambers matt.chamber...@gmail.com wrote: That's not an msconvert warning. Msconvert would handle his MRM data fine as mzML, not mzXML. Does TPP work with mzML chromatograms yet? -Matt On 2/1/2012 3:35 PM, Joseph Slagel wrote: Harry, I'm not sure I can be of any more help. I'd suggest you forward your question to the ProteoWizard's mailing list (proteowizard-supp...@lists.sourceforge.net mailto:proteowizard-supp...@lists.sourceforge.netmailto:supp...@proteowizard.org) and I'm sure you'll get a answer. -Joe On Tue, Jan 31, 2012 at 11:18 AM, Harry mrl...@gmail.com mailto:mrl...@gmail.com wrote: Hello Joe, Thank you for replying my question. The error message I got looks like this: ... Preprocessing function 97 !!Warning!!: ignoring function 97 with type MRM Preprocessing function 98 !!Warning!!: ignoring function 98 with type MRM Preprocessing function 99 !!Warning!!: ignoring function 99 with type MRM no scans found, exiting with error END OUTPUT RETURN CODE:65280 ## End Command Execution ## # All finished at Tue Jan 31 10:57:14 2012 # END COMMAND BLOCK I also tried msconvert. The program did generate a mzXML file from the raw data, but there is no actual data (MRM transitions and their signal intensities) in the mzXML file. Would it be more useful to you to see the problem if I send you the mzXML file? Thank you for your time. Harry On Jan 31, 10:40 am, Joseph Slagel joseph.sla...@systemsbiology.org mailto:joseph.sla...@systemsbiology.org wrote: Harry, What error did you get? Did it look anything like: [Tue Jan 31 12:33:25 2012] EXECUTING: c:\Inetpub\tpp-bin\ReAdW -v -- mzXML c:/Inetpub/wwwroot/ISB/data/12032011_60min_PaG_XC_HP101_01.raw OUTPUT: The system cannot find message text for message number 0x2331 in the message file for Application. If so, then please try using msconvert instead of ReAdW. We're no longer supporting or bundling this program with TPP. -Joe On Mon, Jan 30, 2012 at 1:45 PM, Harry mrl...@gmail.com mailto:mrl...@gmail.com wrote: Hello, I was trying to use the mzXML conversion tool in PPT to convert some MRM raw data acquired on a Waters Xevo through direct infusion. The program could not do it. Has anybody had similar problem? Thank you for any ideas and suggestions. Harry -- 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] Re: Help please: having trouble converting Waters MRM raw data to mzXML
I'm not sure what you mean by column head[er]s. What context are you viewing the mzML in? -Matt On 2/2/2012 12:58 PM, Harry wrote: Hello Matt, Thanks for the comments. I tried converting the raw data to mzML instead of mzXML as well. It didn't work. All I got in the mzML file is the column heads, but no content. Harry On Feb 1, 1:40 pm, Matthew Chambersmatt.chamber...@gmail.com wrote: That's not an msconvert warning. Msconvert would handle his MRM data fine as mzML, not mzXML. Does TPP work with mzML chromatograms yet? -Matt On 2/1/2012 3:35 PM, Joseph Slagel wrote: Harry, I'm not sure I can be of any more help. I'd suggest you forward your question to the ProteoWizard's mailing list (proteowizard-supp...@lists.sourceforge.net mailto:proteowizard-supp...@lists.sourceforge.netmailto:supp...@proteowizard.org) and I'm sure you'll get a answer. -Joe On Tue, Jan 31, 2012 at 11:18 AM, Harrymrl...@gmail.commailto:mrl...@gmail.com wrote: Hello Joe, Thank you for replying my question. The error message I got looks like this: ... Preprocessing function 97 !!Warning!!: ignoring function 97 with type MRM Preprocessing function 98 !!Warning!!: ignoring function 98 with type MRM Preprocessing function 99 !!Warning!!: ignoring function 99 with type MRM no scans found, exiting with error END OUTPUT RETURN CODE:65280 ## End Command Execution ## # All finished at Tue Jan 31 10:57:14 2012 # END COMMAND BLOCK I also tried msconvert. The program did generate a mzXML file from the raw data, but there is no actual data (MRM transitions and their signal intensities) in the mzXML file. Would it be more useful to you to see the problem if I send you the mzXML file? Thank you for your time. Harry On Jan 31, 10:40 am, Joseph Slageljoseph.sla...@systemsbiology.org mailto:joseph.sla...@systemsbiology.org wrote: Harry, What error did you get? Did it look anything like: [Tue Jan 31 12:33:25 2012] EXECUTING: c:\Inetpub\tpp-bin\ReAdW -v -- mzXML c:/Inetpub/wwwroot/ISB/data/12032011_60min_PaG_XC_HP101_01.raw OUTPUT: The system cannot find message text for message number 0x2331 in the message file for Application. If so, then please try using msconvert instead of ReAdW. We're no longer supporting or bundling this program with TPP. -Joe On Mon, Jan 30, 2012 at 1:45 PM, Harrymrl...@gmail.commailto:mrl...@gmail.com wrote: Hello, I was trying to use the mzXML conversion tool in PPT to convert some MRM raw data acquired on a Waters Xevo through direct infusion. The program could not do it. Has anybody had similar problem? Thank you for any ideas and suggestions. Harry -- 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: Help please: having trouble converting Waters MRM raw data to mzXML
Thanks for your help Joe. Harry On Feb 1, 1:35 pm, Joseph Slagel joseph.sla...@systemsbiology.org wrote: Harry, I'm not sure I can be of any more help. I'd suggest you forward your question to the ProteoWizard's mailing list ( proteowizard-supp...@lists.sourceforge.net supp...@proteowizard.org) and I'm sure you'll get a answer. -Joe On Tue, Jan 31, 2012 at 11:18 AM, Harry mrl...@gmail.com wrote: Hello Joe, Thank you for replying my question. The error message I got looks like this: ... Preprocessing function 97 !!Warning!!: ignoring function 97 with type MRM Preprocessing function 98 !!Warning!!: ignoring function 98 with type MRM Preprocessing function 99 !!Warning!!: ignoring function 99 with type MRM no scans found, exiting with error END OUTPUT RETURN CODE:65280 ## End Command Execution ## # All finished at Tue Jan 31 10:57:14 2012 # END COMMAND BLOCK I also tried msconvert. The program did generate a mzXML file from the raw data, but there is no actual data (MRM transitions and their signal intensities) in the mzXML file. Would it be more useful to you to see the problem if I send you the mzXML file? Thank you for your time. Harry On Jan 31, 10:40 am, Joseph Slagel joseph.sla...@systemsbiology.org wrote: Harry, What error did you get? Did it look anything like: [Tue Jan 31 12:33:25 2012] EXECUTING: c:\Inetpub\tpp-bin\ReAdW -v -- mzXML c:/Inetpub/wwwroot/ISB/data/12032011_60min_PaG_XC_HP101_01.raw OUTPUT: The system cannot find message text for message number 0x2331 in the message file for Application. If so, then please try using msconvert instead of ReAdW. We're no longer supporting or bundling this program with TPP. -Joe On Mon, Jan 30, 2012 at 1:45 PM, Harry mrl...@gmail.com wrote: Hello, I was trying to use the mzXML conversion tool in PPT to convert some MRM raw data acquired on a Waters Xevo through direct infusion. The program could not do it. Has anybody had similar problem? Thank you for any ideas and suggestions. Harry -- 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] Building on OS X 10.7.3
Hi all, I trying to build version TPP 4.5.1 on OS X 10.7.3 and after make all I end up getting the following: g++ -D__LINUX__ -DDEFAULT_TPP_INSTALL_ROOT=\/usr/local/tpp/\ - D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D__INTEL__ -DINLINING - DTPPLIB -fPIC -I. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/gzstream -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ libarchive-2.2.7/libarchive -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/expat-2.0.1/lib -I/Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ fann-2.0.0/src/include -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/gsl-1.14 -I /opt/local/ include/ -iprefix /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/ -iwithprefix pwiz/data/msdata -iwithprefix pwiz/data -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz - iwithprefix pwiz -iwithprefix pwiz/utility/misc -iwithprefix pwiz/ utility/math -I/Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/ src/../extern/boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -iwithprefix libraries/boost_aux -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/Parsers/ramp -iwithprefix libraries/ libsvm-3.0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE - DPWIZ_USER_VERSION_INFO_H=\common/TPPVersion.h\ -c -O2 -o /Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ Serializer_mzXML.pwiz.o /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/data/ msdata/Serializer_mzXML.cpp g++ -D__LINUX__ -DDEFAULT_TPP_INSTALL_ROOT=\/usr/local/tpp/\ - D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D__INTEL__ -DINLINING - DTPPLIB -fPIC -I. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/. -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/gzstream -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ libarchive-2.2.7/libarchive -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/expat-2.0.1/lib -I/Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ fann-2.0.0/src/include -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../build/darwin/gsl-1.14 -I /opt/local/ include/ -iprefix /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/ -iwithprefix pwiz/data/msdata -iwithprefix pwiz/data -I/Users/OK/Downloads/ TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz - iwithprefix pwiz -iwithprefix pwiz/utility/misc -iwithprefix pwiz/ utility/math -I/Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/ src/../extern/boost_1_45_0/boost -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/boost_1_45_0 -I/Users/OK/ Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/. -iwithprefix libraries/boost_aux -I/Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/Parsers/ramp -iwithprefix libraries/ libsvm-3.0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE - DPWIZ_USER_VERSION_INFO_H=\common/TPPVersion.h\ -c -O2 -o /Users/ OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../build/darwin/ SHA1.pwiz.o /Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/ src/../extern/ProteoWizard/pwiz/pwiz/utility/misc/SHA1.cpp In file included from /Users/OK/Downloads/TPP-4.5.1/ trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/utility/ misc/SHA1.cpp:10: /Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/src/../extern/ ProteoWizard/pwiz/pwiz/utility/misc/endian.hpp:66:2: error: #error Unsupported platform: probably need a platform-specific define above. make: *** [/Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/ src/../build/darwin/SHA1.pwiz.o] Error 1 Can someone advice? Thanks, 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
