PEAKS: Brucker

Bruker produces CompassXport, a free tool to convert Bruker native data to mzXML. It handles .baf (MicroTOF), .yep (Esquire), fid files (flex) and AutoXecute run from LCMADLI(autoFlex, ultraFlex) formats. This tool is also a plug-in for PEAKS. When compassxport is installed, PEAKS seamlessly reads in the Bruker data directly.

Bruker's tool is not shareware but they allow it to be used for free if the person who installs the software agreesto the license agreement. To get the tool you will need a login and password to Bruker's site (http://www.brukerdaltonics.com/) Click on "Login/out" that is located on the top right hand corner. Have your Bruker login and password ready. If you don't have a username/password for the bruker website, you can sign up for free.

After you have logged-in, select "Library" under the "NAVIGATION" header on the top lefthand corner of Bruker's website. Click on "Downloads & Patches". On their site you will see a picture of two file folders. Select the one called "Software". Now there will be a page with several file folders. Click on the one called "Compass". Now select the file folder named "CompassXport". This will open a page with files to be downloaded. To get the tool select the button beside "CompassXport SFX - Installation file". This will open the "download manager" window. Click on the "compassxportsfx1.x.exe" file name shown in blue. This will begin the download. It may be helpful to download the "CompassXport SFX - FAQ" (.pdf) and the "CompassXport SFX - Release Notes" (.txt) for the installation and operation documentation. Please be sure to have the Adobe Acrobat Reader installed to view the "CompassXport-FAQ.pdf".

Go to the place where you saved the "compassxportsfx1.x.exe" file and double click on the icon. Follow the installation instructions. Bruker has done a good job to make the installation as painless as possible. Ensure that you have logged on to your computer with administrative rights, otherwise the installation will fail.

If PEAKS is open, close it and open again. When setting up a project you may now go ahead and add your Bruker files to projects and start processing them.

Though PEAKS uses compassXport automatically, behind the scenes, there may be some occasions where we want to use it manually. Open a command prompt window to run the program by selecting, "Start Menu" > "Programs" > "Accessories" > "Command Prompt". A dos window will open. Type CompassXport and press the enter key to execute the program. Doing this, simply displays some information about how to use the tool. To convert data, you'll have to tell the tool the path(location) of your data. An example of a typical command line would be:

The "-a" parameter is the file to be converted and the location of the file, in this case it is in the "BAF" file and is called "analysis.baf". The "-o" parameter is the location and filename of where the resultant XML file is to be saved. There's more information in the README and documentation that Bruker provides.

PEAKS can open the mzXML files that compassXport produces, even when run manually this way.

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Overview De Novo Sequencing Database Search Multiple Database Search Sequence Homology PTM Quantification RAW Data Tech Support Our Research User Comments User Research Download Demo Request Prices	Superior de novo sequencing and protein ID Software PEAKS Bruker Data to mzXML Conversion PEAKS can load data from Bruker mass spectrometers provided that the CompassXport software is installed on the same computer. If loading .fid files, which are stored in a network of folders, select the top level folder to load them all at once. Bruker produces CompassXport, a free tool to convert Bruker native data to mzXML. It handles .baf (MicroTOF), .yep (Esquire), fid files (flex) and AutoXecute run from LCMADLI(autoFlex, ultraFlex) formats. This tool is also a plug-in for PEAKS. When compassxport is installed, PEAKS seamlessly reads in the Bruker data directly. Installing CompassXport for PEAKS Bruker's tool is not shareware but they allow it to be used for free if the person who installs the software agreesto the license agreement. To get the tool you will need a login and password to Bruker's site (http://www.brukerdaltonics.com/) Click on "Login/out" that is located on the top right hand corner. Have your Bruker login and password ready. If you don't have a username/password for the bruker website, you can sign up for free. After you have logged-in, select "Library" under the "NAVIGATION" header on the top lefthand corner of Bruker's website. Click on "Downloads & Patches". On their site you will see a picture of two file folders. Select the one called "Software". Now there will be a page with several file folders. Click on the one called "Compass". Now select the file folder named "CompassXport". This will open a page with files to be downloaded. To get the tool select the button beside "CompassXport SFX - Installation file". This will open the "download manager" window. Click on the "compassxportsfx1.x.exe" file name shown in blue. This will begin the download. It may be helpful to download the "CompassXport SFX - FAQ" (.pdf) and the "CompassXport SFX - Release Notes" (.txt) for the installation and operation documentation. Please be sure to have the Adobe Acrobat Reader installed to view the "CompassXport-FAQ.pdf". Go to the place where you saved the "compassxportsfx1.x.exe" file and double click on the icon. Follow the installation instructions. Bruker has done a good job to make the installation as painless as possible. Ensure that you have logged on to your computer with administrative rights, otherwise the installation will fail. If PEAKS is open, close it and open again. When setting up a project you may now go ahead and add your Bruker files to projects and start processing them. Using CompassXport manually Though PEAKS uses compassXport automatically, behind the scenes, there may be some occasions where we want to use it manually. Open a command prompt window to run the program by selecting, "Start Menu" > "Programs" > "Accessories" > "Command Prompt". A dos window will open. Type CompassXport and press the enter key to execute the program. Doing this, simply displays some information about how to use the tool. To convert data, you'll have to tell the tool the path(location) of your data. An example of a typical command line would be: CompassXport.exe -a BAF/analysis.baf -o BAF/analysis.XML The "-a" parameter is the file to be converted and the location of the file, in this case it is in the "BAF" file and is called "analysis.baf". The "-o" parameter is the location and filename of where the resultant XML file is to be saved. There's more information in the README and documentation that Bruker provides. PEAKS can open the mzXML files that compassXport produces, even when run manually this way. If any errors or inaccuracies are noted from this page please contact us.