This is the simplest example where analysis. Introduction tutorial finnee blog. Actually for this program if you just type compassxport on the command line the instructions will popup as shown in the screenshot below.

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If you need to find the CompassXport program to place it in the folder you should be able to find it in the following directory C: However, when we installed the program for the first time this apparently was not the case and we needed to place the program in the folder with the data files in order to invoke the program.

I have every confidence that this type of open source effort will speed up scientific research.

The registration appeared to work on the second XP computer that we installed CompassXport on and the CompassXport command worked and was recognized from any directory.

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Type cd "your path to the folder. Fill in your details below or click an icon to log in: It is a revolution I think. CompassXport can compassxpprt download after registering for free from the Bruker web site.

Bruker Yep files and error ID 2 (Page 1) - Bugs and Troubleshooting - mMass Support Forum

Once installed, when you type the CompassXport command on the command line your computer should recognize it.

Compassxporh is the simplest example where analysis. Actually DOS is case insensitive so there is no need to capitalize the program name or the folder names.

Bellow is compsssxport screenshot of the command line execution CompassXport -a analysis. Thanks to CompassXport we can now give our clients native data files and point them to Bruker and Insilicos to get the converter and the viewer.

Mass Spectrometry Software Support

Now you can use the free Insilicos viewer to peruse your new mzXML datafile. Some search engine sellers or MS vendors may fear this advance, but what it will really compassxprt is that more people will have access to MS data and more people will be able to search their own data, and hence more search engine software will be sold.

Once extracted, click on the setup file as shown above and the program will install on your computer with a standard install shield as shown below. You will need to click on the login button at the top to register for an account. A common file format has been a dream of mass spectrometrists since the second instrument company made a mass spectrometer.

You can download CompassXport for free from Bruker. In our case we did not manage to run it and used CompassXport instead that is specific for Bruker file. Many algorithms dedicate to the analysis of mass spectrometer data sets have been made possible by the work of few groups to develop and promote the use of a vendor independent, easily readable and open file format.

I used CompassXport with two different computers, one using Windows 8, the other using Window 10 without major problems. Some of compassxpoort typing is shown in the command line screenshots below.

Converting Bruker files to the mzML format using CompassXport. | finnee blog

You will need to register at the Bruker web site to be able to access the download page. Bruker also includes some visual basic scripts with compassxpogt download that may be useful, but we have not tried them.

You can convert entire groups of files and specify output names.

This is the initial screenshot of the folder containing the. Nowadays, mzML is recognized as the standard for vendor independent MS data format. You can simply copy and paste it in a new function in Matlab. The structure of mzML files as well as approaches to read them using Matlab will be explore in the next post.

Now anyone can read native Bruker and some Agilent files.


If it is a proteomics type data file, several on-line ccompassxport engines will accept this new file format for searching, theGPM is one that you can try. This format is now accepted by instrument manufacturers and they often provide freeware compassdport converting their proprietary file to the mzML format.

A tutorial can be found in IonSource. A complete list of software that are available for each instrument manufacturer can be found in the website of the SPC.



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