PEAKS: ABI QSTAR/QTRAP

The MSX plug-in (optional) to PEAKS Studio allows us to import QSTAR .wiff data directly into PEAKS. MSX is developed by Infochromics, a spin off of the MDS companies. You can purchase a license, at cost, from BSI. This converter has an advantage over the others in that it bypasses the 'export to mascot' dll library -- and therefore some users suggest it improves data integrity. MSX can be downloaded from the same location as the PEAKS Studio Demo. Please contact your rep for details. Once MSX is installed, simply choose "Import .wiff raw data" from the file menu in PEAKS Studio.

If you choose not to purchase the MSX plug-in, you may still convert .wiff files into a format useable by PEAKS. Details on some converters are provided below. In all cases please make sure to give PEAKS non-centroided data.

The Sashimi Project is an attempt to standardize all MS data to a single format that everyone can read. They have developed converters that read all kinds of data and convert it to an XML format called mzXML. PEAKS can read mzXML files directly. Simply click the following link to download mzSTAR from the sashimi project's website: http://cvs.sourceforge.net/viewcvs.py/*checkout*/sashimi/mzStar/mzStar.exe?rev=1.13. This will open a download window. Save the executable to a convient location.Try this link to see if there's a newer version

The file may be called "mzStar.13". Rename it to "mzStar.exe" and double click on its icon. This window (right) appears. Please note, put mzSTAR on the same system that Analyst software is installed on. If you see the error message "ActiveX component can’t create object”, it's because mzStar can't find the Analyst libraries it needs. Moving it to the computer on which analyst is installed should fix the problem.

The files to be converted will appear in the second column and the converted mzXML will appear in the third column. Be sure to leave the “Peak Cutoff” and “Centroid?” options “0” and unchecked respectively. PEAKS will give better results with more data to sift through. By clicking the "Convert" button the selected files will be converted to mzXML.

Andreas M. Boehm and Albert Sickmann from Unversitaet Wuerzburg have created this tool with assistance from Robert P Galvin at Applied Biosystems. The tool can be downloaded from: http://sourceforge.net/projects/protms/. Make sure you download the one built for your version of Analyst. Also you can grab the WIFF2DTA_1108.HLP file, which is the help document. This tool requires that Analyst be on the same computer that it is installed on. This is a windows based version and can be easily run by double clicking the icon. If you do not have Analyst or XYMathUtils on your computer you will get the message “You need at least 1.11 of XYMathUtils for processing QTrap data.

QTrap processing will be deactivated.” in the “Version Check” pop-up window. The files that are to be converted must be on the computer you are running the tool and not a network drive.. This tool requires that Analyst be on the same computer that it is installed on.

To convert wiff files from a tree of folders check the “tree of folders?” check box. To put the converted files in one folder check the “all in one folder?” check box that appears when you check the “tree of folders?” option. Note, that the “destination” folder can be a network location and need not be on the computer the tool is installed in. Noteably, the tool is useful in a high-throughput environment, because all it's funtions and options are available through command-line.

The ccwiffer tool will convert wiff files to mzXML or mzData. The name is short for “Charleston Core wiff Converted” and it is reputed to be faster then all other conversion tools (perhaps with the exception of MSX, no test has been done).

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De Novo Sequencing Protein ID PTM Seq. Tag Search Raw Data Tech Support Request Prices Try PEAKS Our Research User Comments	Superior de novo sequencing and protein ID Software PEAKS Converting wiff files from the QStar and QTrap The MSX plug-in (optional) to PEAKS Studio allows us to import QSTAR .wiff data directly into PEAKS. MSX is developed by Infochromics, a spin off of the MDS companies. You can purchase a license, at cost, from BSI. This converter has an advantage over the others in that it bypasses the 'export to mascot' dll library -- and therefore some users suggest it improves data integrity. MSX can be downloaded from the same location as the PEAKS Studio Demo. Please contact your rep for details. Once MSX is installed, simply choose "Import .wiff raw data" from the file menu in PEAKS Studio. If you choose not to purchase the MSX plug-in, you may still convert .wiff files into a format useable by PEAKS. Details on some converters are provided below. In all cases please make sure to give PEAKS non-centroided data. mzSTAR - mzXML method The Sashimi Project is an attempt to standardize all MS data to a single format that everyone can read. They have developed converters that read all kinds of data and convert it to an XML format called mzXML. PEAKS can read mzXML files directly. Simply click the following link to download mzSTAR from the sashimi project's website: http://cvs.sourceforge.net/viewcvs.py/checkout/sashimi/mzStar/mzStar.exe?rev=1.13. This will open a download window. Save the executable to a convient location.Try this link to see if there's a newer version The file may be called "mzStar.13". Rename it to "mzStar.exe" and double click on its icon. This window (right) appears. Please note, put mzSTAR on the same system that Analyst software is installed on. If you see the error message "ActiveX component can’t create object”, it's because mzStar can't find the Analyst libraries it needs. Moving it to the computer on which analyst is installed should fix the problem. The files to be converted will appear in the second column and the converted mzXML will appear in the third column. Be sure to leave the “Peak Cutoff” and “Centroid?” options “0” and unchecked respectively. PEAKS will give better results with more data to sift through. By clicking the "Convert" button the selected files will be converted to mzXML. Wiff2dta method Andreas M. Boehm and Albert Sickmann from Unversitaet Wuerzburg have created this tool with assistance from Robert P Galvin at Applied Biosystems. The tool can be downloaded from: http://sourceforge.net/projects/protms/. Make sure you download the one built for your version of Analyst. Also you can grab the WIFF2DTA_1108.HLP file, which is the help document. This tool requires that Analyst be on the same computer that it is installed on. This is a windows based version and can be easily run by double clicking the icon. If you do not have Analyst or XYMathUtils on your computer you will get the message “You need at least 1.11 of XYMathUtils for processing QTrap data. QTrap processing will be deactivated.” in the “Version Check” pop-up window. The files that are to be converted must be on the computer you are running the tool and not a network drive.. This tool requires that Analyst be on the same computer that it is installed on. To convert wiff files from a tree of folders check the “tree of folders?” check box. To put the converted files in one folder check the “all in one folder?” check box that appears when you check the “tree of folders?” option. Note, that the “destination” folder can be a network location and need not be on the computer the tool is installed in. Noteably, the tool is useful in a high-throughput environment, because all it's funtions and options are available through command-line. ccwiffer method The ccwiffer tool will convert wiff files to mzXML or mzData. The name is short for “Charleston Core wiff Converted” and it is reputed to be faster then all other conversion tools (perhaps with the exception of MSX, no test has been done). The wiff conversion tool is free and can be downloaded from http://sourceforge.net/projects/ccwiffer/ by clicking the “cwiff.exe” file. When you download the tool you will see that the file is called “ccwiff.1” (with the “1” being the version number which changes for time to time). The name of the file must be changed to ccwiff.exe before it is useable. Double click on the ccwiff.exe icon and program with start. Be sure to have the Analyst software on the same computer as this tool or run-time errors will result. The interface is shown above. The use of this tool is explained well in the manual. The manual site can be found at: http://charlestoncore.musc.edu/docs/ccwiffer/usermanual.html. When you are converting the data make sure that no preprocessing options are selected, as this will have a negative impact on the results. If any errors or inaccuracies are noted from this page please contact us.