Error In Converting Raw To Mzxml
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Thermo Q-Exactive raw files in mzXML or mzML? Cheers, Frank I would like to use the TPP for spectra identificationbut it faild to transform the raw files. Topics Mass Spectrometry https://www.researchgate.net/post/Is_there_anyone_who_knows_a_free_program_to_transform_Thermo_Q-Exactive_raw_files_in_mzXML_or_mzML_Cheers_Frank × 917 Questions 14,674 Followers Follow Feb 29, 2012 Share Facebook Twitter LinkedIn https://github.com/PedrioliLab/ReAdW Google+ 2 / 0 All Answers (9) Eugene Melamud Have you had any luck with ReAdW? It works well with regular Exactive, not sure if it works with q. Feb 29, 2012 Frank Schmidt · University of Greifswald Hi Eugene, it did not worked with q. Cheers, Frank Feb 29, 2012 Roman Fischer · error in University of Oxford MSConvert may work...does with Velos data... Cheers, Roman Feb 29, 2012 Markus Hollmann · University of Duisburg-Essen mscovert works for me with QExactive. dont forget to install the software on the same PC as Xcalibur. usually those convertion tools need some files from the original software Mar 1, 2012 Alexander Chizhov · Russian Academy of Sciences To be correct, N- and O- chains have error in converting to be removed and analyzed separately. For methods, see e.g., papers of A. Dell and H. Morris Mar 2, 2012 Roman Fischer · University of Oxford yes MSFilereader needs to be there and the newest version also works with Win7 32/64 bit. XCalibur will only work on Win7 32 bit though. If you have MSFilereader and MSConvert installed, you can simply use this script: @ECHO OFF FOR %%A IN (%*) DO ( ECHO ** ECHO ** Converting %%A to mgf ECHO ** Output to %%~dpA ECHO **" "C:\Documents and Settings\Administrator\Desktop\thermo_msconvert\pwiz\msconvert" %%A -o %%~fsA\..\ --mgf --verbose --filter "threshold count 200 most-intense [2,2]" ) ECHO DONE here you have to change the path for the msconvert.exe on your computer. Just open a texteditor...paste the lines above and save as anyname.cmd ...then you can drag an drop your rawfile onto the .cmd file and it will generate a mgf in the same folder where your raw file is. It will only use the top200 peaks per MSMS. If you need mzxml simply replace mgf with mzxml...this script was written by David Trudgian. Cheers, Roman Mar 2, 2012 Ishtiaq Ahmad · University of Amsterdam Windows Solution: Here is an other in one http://compbio.cs.princeton.edu/p
Sign in Pricing Blog Support Search GitHub This repository Watch 3 Star 6 Fork 4 PedrioliLab/ReAdW Code Issues 0 Pull requests 0 Projects 0 Pulse Graphs Convert ThermoFinningan RAW mass spectrometry files to the mzXML format 33 commits 1 branch 0 releases Fetching contributors LGPL-3.0 C 57.2% C++ 42.7% Shell 0.1% C C++ Shell Clone or download Clone with HTTPS Use Git or checkout with SVN using the web URL. Open in Desktop Download ZIP Find file Branch: master Switch branches/tags Branches Tags master Nothing to show Nothing to show New pull request Fetching latest commit… Cannot retrieve the latest commit at this time. Permalink Failed to load latest commit information. bin Get rid of instrument model enumeration and simply pass read instrume… Jun 21, 2016 scripts Update binaries, readme, and script to reflect no longer using "--mzX… Oct 29, 2014 src Get rid of instrument model enumeration and simply pass read instrume… Jun 21, 2016 .gitignore Added .gitignore file for VS temporary files Oct 31, 2014 LICENSE Initial commit Oct 29, 2014 README.md fix binary files download link Oct 5, 2016 README.md ReAdW Description Convert ThermoFinningan RAW mass spectrometry files to the mzXML format[1]. Originally a part of the Trans-Proteomic Pipeline Dependencies ReAdW requires either Xcalibur or MSFileReader to be installed or minimally just the three DLLs: XRawfile2.dll, fileio.dll, fregistry.dll. MSFileReader can be downloaded by creating an account with ThermoFischer Scientific. Once registered you will find the software under "Utility Software". Binaries Two binaries are available depending on which dependency is installed on your system: The MSFileReader compatible is here The Xcalibur compatible one is here Note: the binaries have been tested to w