Hey, We have Perkin elmer GC-MS which is handled with turbomass software, in which there is no tool to prepare report for peaks available in chronograph. Is there any freeware to produce the report files in PDF or Excel?
Typically the freely downloadable AMDIS Tool: http://chemdata.nist.gov/mass-spc/amdis/downloads/ would handle your Turbomass PE Generated raw data files. From AMDIS you can save the peak properties (Area, qualifier ions etc) easily as Excel. PDF is not useful and is not recommended as it would be like a image (unless you want the chromatographs for publications etc.). If not, then all softwares such as Turbomass would have export/ convert option to .netCDF or .ASCII options (check with their manual or call Tech Support to figure out!) and see if you can! If not then use tools such as those described below (Proteowizard, Mass++) to get the files in .mzXML or .mzML. Once in these formats, easy to save as Excel or .csv or .text format and so on.
Please use Proteowizard's MS Convert Tool for free: http://proteowizard.sourceforge.net/downloads.shtml and with the .data format specific version. Using this you can convert the .data format to most software readable .mzXML or .mzML formats which then can be used for all kind of down stream analyses such as mzMINE (http://mzmine.github.io/), or say Mass++ (http://www.shimadzu.co.jp/aboutus/ms_r/archive/en/index.html) where both can read any common file formats and both from GC-MS and LC-MS. Also, Mass++ can read .data formats and can convert to .mzXML files too.
Also on your platforms specific file for your MS/MS instrument you MUST find a file convert option allowing you to go from .data to .cdf or .netcdf (which is fine for NIST DB) or .ASCII etc. But then, still you need to go to ProteoWizard to go from .cdf to .mzXML (most popular and recommended) or mzML to use for further analysis.
"OpenMS/ OpenChrome" though free bit tricky and messy with having to download a lot of add-ins or plugins to make things work in a step wise manner.
If you are a Linux fan, then MASSyPup64 from Dr. Robert Winkler (http://www.lababi.bioprocess.org/index.php/14-sample-data-articles/78-massypup) is what you may go to!
Other tools for filtering and analysis may be sought here: Further, all freely available tools, software, and databases from 2014-2015 for your analyses have also been recently summarized/ reviewed by us at Updates in metabolomics tools and resources: 2014–2015 (http://onlinelibrary.wiley.com/doi/10.1002/elps.201500417/abstract), please check out the Table-1 and find your tools!!! : ) In this review, you would also find tools other than R, metaXCMS, MAVEN and so on.
Hope it helps.
Thanks, Biswa
Typically the freely downloadable AMDIS Tool: http://chemdata.nist.gov/mass-spc/amdis/downloads/ would handle your Turbomass PE Generated raw data files. From AMDIS you can save the peak properties (Area, qualifier ions etc) easily as Excel. PDF is not useful and is not recommended as it would be like a image (unless you want the chromatographs for publications etc.). If not, then all softwares such as Turbomass would have export/ convert option to .netCDF or .ASCII options (check with their manual or call Tech Support to figure out!) and see if you can! If not then use tools such as those described below (Proteowizard, Mass++) to get the files in .mzXML or .mzML. Once in these formats, easy to save as Excel or .csv or .text format and so on.
Please use Proteowizard's MS Convert Tool for free: http://proteowizard.sourceforge.net/downloads.shtml and with the .data format specific version. Using this you can convert the .data format to most software readable .mzXML or .mzML formats which then can be used for all kind of down stream analyses such as mzMINE (http://mzmine.github.io/), or say Mass++ (http://www.shimadzu.co.jp/aboutus/ms_r/archive/en/index.html) where both can read any common file formats and both from GC-MS and LC-MS. Also, Mass++ can read .data formats and can convert to .mzXML files too.
Also on your platforms specific file for your MS/MS instrument you MUST find a file convert option allowing you to go from .data to .cdf or .netcdf (which is fine for NIST DB) or .ASCII etc. But then, still you need to go to ProteoWizard to go from .cdf to .mzXML (most popular and recommended) or mzML to use for further analysis.
"OpenMS/ OpenChrome" though free bit tricky and messy with having to download a lot of add-ins or plugins to make things work in a step wise manner.
If you are a Linux fan, then MASSyPup64 from Dr. Robert Winkler (http://www.lababi.bioprocess.org/index.php/14-sample-data-articles/78-massypup) is what you may go to!
Other tools for filtering and analysis may be sought here: Further, all freely available tools, software, and databases from 2014-2015 for your analyses have also been recently summarized/ reviewed by us at Updates in metabolomics tools and resources: 2014–2015 (http://onlinelibrary.wiley.com/doi/10.1002/elps.201500417/abstract), please check out the Table-1 and find your tools!!! : ) In this review, you would also find tools other than R, metaXCMS, MAVEN and so on.
Hope it helps.
Thanks, Biswa
Dr Biswapriya Biswavas Misra gave you a very exhaustive and pertinent answer and I have nothing more to add to his comments.However, If I am correct, Turbomass software includes a subprogram entitled Communiqué reports that should provide directly what you are looking for. It provides both qualitative and quantitative reports for all identified peaks. It includes a report editor with several pre-filled templates.
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