PEAKS: Thermo

PEAKS Studio, PEAKS Client and PEAKS Viewer can open Thermo RAW data, and .dta files. In order to load RAW data, PEAKS must be installed on the same computer as Thermo's XCalibur software. To open the RAW data file, simply start PEAKS and select 'Open' from the 'File' menu. All ms/ms scans will be listed by their precursor m/z, charge state (if the RAW file contained this information) and retention time. If the RAW file does not contain precursor charge state, one must use the Data Refine tool to calculate it.

PEAKS also reads .dta files produced by Bioworks. One can open a single .dta file or a whole folder full of .dta files, using 'Load Directory' from the file menu. PEAKS can be call upon from within Bioworks to load some selected .dta files. Consult your Bioworks user's manual for instructions.

Thermo RAW data can also be converted to mzXML for use with PEAKS. The "Sashimi Project" provides a tool, called ReAdW for this purpose. For more information concerning this format visit http://sashimi.sourceforge.net/index.html.

A download for this tool can be found at:
http://sashimi.sourceforge.net/software_glossolalia.html#ReAdW.
Click the "ReAdW.exe" link on the web site and save the executable file to a convenient location. The software can not be run directly in windows. It only has a command line interface. This means that a command prompt window must be opened. To do this click the "Start" button on your windows desktop. Select the "Run..." option and the space provided beside "Open:" either type "cmd" for Windows XP/2000/NT or "command" if your operating system is very old. Change the directory that you are in to the one where you saved the "ReAdW.exe" executable. As you see in the window (right) the file was saved to the desktop. Type in "ReAdW.exe", a space,then the RAW file location or path, another space and finally either "c" or "p". The entire input with look something like the this:

The "c" option means "centroid" and the "p" option means "profile". Be sure to use unpreprocessed data with PEAKS, so use the "p" option when converting to mzXML. PEAKS has its own preprocess function that is tuned to give the best results for our de novo sequencing algorithm.

The resulting mzXML files will be written to the same folder where the RAW file is and be called the same name but with a ".mzXML" ending. As in the case above there will be a "sample.raw" and a "sample.mzXML" in the folder.

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De Novo Sequencing Protein ID inChorus PTM Seq. Tag Search Raw Data Download Demo Request Prices Tech Support Our Research User Comments	Superior de novo sequencing and protein ID Software PEAKS Loading Thermo RAW Data PEAKS Studio, PEAKS Client and PEAKS Viewer can open Thermo RAW data, and .dta files. In order to load RAW data, PEAKS must be installed on the same computer as Thermo's XCalibur software. To open the RAW data file, simply start PEAKS and select 'Open' from the 'File' menu. All ms/ms scans will be listed by their precursor m/z, charge state (if the RAW file contained this information) and retention time. If the RAW file does not contain precursor charge state, one must use the Data Refine tool to calculate it. PEAKS also reads .dta files produced by Bioworks. One can open a single .dta file or a whole folder full of .dta files, using 'Load Directory' from the file menu. PEAKS can be call upon from within Bioworks to load some selected .dta files. Consult your Bioworks user's manual for instructions. ReAdW conversion method Thermo RAW data can also be converted to mzXML for use with PEAKS. The "Sashimi Project" provides a tool, called ReAdW for this purpose. For more information concerning this format visit http://sashimi.sourceforge.net/index.html. A download for this tool can be found at: http://sashimi.sourceforge.net/software_glossolalia.html#ReAdW. Click the "ReAdW.exe" link on the web site and save the executable file to a convenient location. The software can not be run directly in windows. It only has a command line interface. This means that a command prompt window must be opened. To do this click the "Start" button on your windows desktop. Select the "Run..." option and the space provided beside "Open:" either type "cmd" for Windows XP/2000/NT or "command" if your operating system is very old. Change the directory that you are in to the one where you saved the "ReAdW.exe" executable. As you see in the window (right) the file was saved to the desktop. Type in "ReAdW.exe", a space,then the RAW file location or path, another space and finally either "c" or "p". The entire input with look something like the this: ReAdW.exe c:\thermo\data\sample.raw p The "c" option means "centroid" and the "p" option means "profile". Be sure to use unpreprocessed data with PEAKS, so use the "p" option when converting to mzXML. PEAKS has its own preprocess function that is tuned to give the best results for our de novo sequencing algorithm. The resulting mzXML files will be written to the same folder where the RAW file is and be called the same name but with a ".mzXML" ending. As in the case above there will be a "sample.raw" and a "sample.mzXML" in the folder. If any errors or inaccuracies are noted from this page please contact us.