[spctools-discuss] converting RAW files to mzXML format
Hi friends, I am getting this message when trying to convert my Thermo Scientific LC-MS generated Raw files to mzXML. c:\Inetpub\tpp-bin\ReAdW -v --mzXML -z c:/Inetpub/wwwroot/ISB/data/ 11-14-11-SS3R3/Rao-SS3R3No1.raw 'c:\Inetpub\tpp-bin\ReAdW' is not recognized as an internal or external command, operable program or batch file. Command FAILED However, I could convert the .raw files to mzML yesterday. Any help is appreciated. Thanks Rao -- 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] converting RAW files to mzXML format
Thanks Joe, I downloaded msconvert but it is not working for some reason. But I finally downloaded a massmatrix converter and it work fantastic. You may suggest the same to anyone interested in conversions. Thanks Rao On Fri, Nov 18, 2011 at 4:17 PM, Joseph Slagel joseph.sla...@systemsbiology.org wrote: Rao, Try using msconvert to do your conversions. We've largely deprecated readw and no longer include it in the TPP installation. If you absolutely have to use it you can still get it from the spctools website. -Joe On Fri, Nov 18, 2011 at 7:58 AM, Rao kottapalli...@gmail.com wrote: Hi friends, I am getting this message when trying to convert my Thermo Scientific LC-MS generated Raw files to mzXML. c:\Inetpub\tpp-bin\ReAdW -v --mzXML -z c:/Inetpub/wwwroot/ISB/data/ 11-14-11-SS3R3/Rao-SS3R3No1.raw 'c:\Inetpub\tpp-bin\ReAdW' is not recognized as an internal or external command, operable program or batch file. Command FAILED However, I could convert the .raw files to mzML yesterday. Any help is appreciated. Thanks Rao -- 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. -- Kameswara Rao Kottapalli, Ph.D. Research Associate Professor Center for Biotechnology and Genomics Texas Tech University 8th Canton, Experimental Sciences Building, Room 101 Lubbock, TX 79409 Phone (O):1-806-742-3722 x 232; (Mob): 1-806-577-9167 -- 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] Converting .RAW files
Dear All, I want to try the cpan module Xcalibur::Rawfile to convert RAW files to mzXML/mgf/PKL. Has anyone tried it? How does it work ? Do i need Xcalibur SDK on the machine(windows vista home premium)? -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@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] Converting .RAW files
I'm fairly certain that you need to have the development kit installed. Looking over the Xcalibur::Rawfile code it pretty clearly calls out an error if its not installed. -joe On Mon, Mar 8, 2010 at 8:50 PM, Amit Kumar Yadav amit007thech...@gmail.comwrote: Dear All, I want to try the cpan module Xcalibur::Rawfile to convert RAW files to mzXML/mgf/PKL. Has anyone tried it? How does it work ? Do i need Xcalibur SDK on the machine(windows vista home premium)? -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.comspctools-discuss%2bunsubscr...@googlegroups.com . For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en. -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206) 732-1362 -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@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] Converting .RAW files
I haven't worked with that Perl module. But I would strongly suggest that you first get the most current version of proteowizard's mscovert working from the command-line, and then run this program as a shell command from perl. msconvert, the recommended raw file converter, is under rapid developlment, and I doubt that the module is keeping track of the latest improvements and bug fixes in that code. So my two cents: save yourself the trouble of going through another layer of indirection and just use msconvert as directly as possible. -Natalie On 3/8/10 8:50 PM, Amit Kumar Yadav wrote: Dear All, I want to try the cpan module Xcalibur::Rawfile to convert RAW files to mzXML/mgf/PKL. Has anyone tried it? How does it work ? Do i need Xcalibur SDK on the machine(windows vista home premium)? -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@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.
