Re: [spctools-discuss] Building on OS X 10.7.3
Hi Oded, the workaround is to comment out conditions for LITTLE_ENDIAN in /extern/ProteoWizard/pwiz/pwiz/utility/misc/endian.hpp: change to: // #if (defined(PWIZ_GCC) defined(__BYTE_ORDER) __BYTE_ORDER==__LITTLE_ENDIAN) || \ // (defined(__DARWIN_BYTE_ORDER) __DARWIN_BYTE_ORDER==__DARWIN_LITTLE_ENDIAN) || \ // (defined(__DARWIN_10_6_AND_LATER) defined(__LITTLE_ENDIAN__)) || \ // (defined(__MINGW32__)) || \ // (defined(__i386__)) || \ // (defined(PWIZ_MSVC)) #define PWIZ_LITTLE_ENDIAN // #endif // #if (defined(PWIZ_GCC) defined(__BYTE_ORDER) __BYTE_ORDER==__BIG_ENDIAN) // #define PWIZ_BIG_ENDIAN // #endif #if defined(PWIZ_LITTLE_ENDIAN) defined(PWIZ_BIG_ENDIAN) #error This isn't happening. #endif #if !defined(PWIZ_LITTLE_ENDIAN) !defined(PWIZ_BIG_ENDIAN) #error Unsupported platform: probably need a platform-specific define above. #endif changing DARWIN_10_6 to 10_7 didn't help. Maybe, someone figured out the correct platform definition for 10.7? Cheers Ulrich On 2012-02-03, at 6:20 AM, Oded wrote: 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/
[spctools-discuss] Re: Help please: having trouble converting Waters MRM raw data to mzXML
Hi Matt, I'm using Excel to open the mzML/mzXML files. What I am trying to do with the mzML/mzXML files is to extract just the MRM transitions and their corresponding signal intensities and use my own MATLAB program to do data analysis. I had been able to use the TPP to convert the Thermo MRM raw data to mzXML files. But so far it has not been working for the Waters MRM raw data. Thanks, Harry On Feb 2, 11:05 am, Matthew Chambers matt.chamber...@gmail.com wrote: 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.
Re: [spctools-discuss] Re: Help please: having trouble converting Waters MRM raw data to mzXML
Wow, I'd never opened an XML file in excel. You definitely can't make sense of mzML like that. I tried it with a 60mb mzML and it froze indefinitely (waited 10 minutes). I don't understand how you did it with mzXML either...did you decode the base64 in MATLAB? I'll privately send you a modified mscat that will accept an optional --chromatograms argument and will output all the chromatograms in an mzML file in fixed-column ASCII form. The output looks like: SRM SIC Q1=130.1 Q3=71.1 sample=1 period=1 experiment=1 transition=0 0.0298 0.0606 0.0912 0.1218 0.1525 0.1832 0.2137 0.2444 ... 0. 0. 200. 0. 0. 0. 0. 0. ... I will commit this updated mscat to pwiz soon. Hope this helps, -Matt On 2/3/2012 12:39 PM, Harry wrote: Hi Matt, I'm using Excel to open the mzML/mzXML files. What I am trying to do with the mzML/mzXML files is to extract just the MRM transitions and their corresponding signal intensities and use my own MATLAB program to do data analysis. I had been able to use the TPP to convert the Thermo MRM raw data to mzXML files. But so far it has not been working for the Waters MRM raw data. Thanks, Harry On Feb 2, 11:05 am, Matthew Chambersmatt.chamber...@gmail.com wrote: 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.comwrote: 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.comwrote: 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.comwrote: 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: Building on OS X 10.7.3
Thanks Ulrich. As always - you got it! All the best, Oded On Feb 3, 7:31 pm, Ulrich auf dem Keller uadkel...@me.com wrote: Hi Oded, the workaround is to comment out conditions for LITTLE_ENDIAN in /extern/ProteoWizard/pwiz/pwiz/utility/misc/endian.hpp: change to: // #if (defined(PWIZ_GCC) defined(__BYTE_ORDER) __BYTE_ORDER==__LITTLE_ENDIAN) || \ // (defined(__DARWIN_BYTE_ORDER) __DARWIN_BYTE_ORDER==__DARWIN_LITTLE_ENDIAN) || \ // (defined(__DARWIN_10_6_AND_LATER) defined(__LITTLE_ENDIAN__)) || \ // (defined(__MINGW32__)) || \ // (defined(__i386__)) || \ // (defined(PWIZ_MSVC)) #define PWIZ_LITTLE_ENDIAN // #endif // #if (defined(PWIZ_GCC) defined(__BYTE_ORDER) __BYTE_ORDER==__BIG_ENDIAN) // #define PWIZ_BIG_ENDIAN // #endif #if defined(PWIZ_LITTLE_ENDIAN) defined(PWIZ_BIG_ENDIAN) #error This isn't happening. #endif #if !defined(PWIZ_LITTLE_ENDIAN) !defined(PWIZ_BIG_ENDIAN) #error Unsupported platform: probably need a platform-specific define above. #endif changing DARWIN_10_6 to 10_7 didn't help. Maybe, someone figured out the correct platform definition for 10.7? Cheers Ulrich On 2012-02-03, at 6:20 AM, Oded wrote: 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/
