which software ur instrument use, because I know chemstation allows copying of files in CSV format for data analysis

I am using FlexControl and FlexAnalysis.

Fabio is that the name of your instrument chromatography software ?

sorry, am not familiar with that software, try and get the user manual, or go to the help on the software. I am more familiar with Glaxie, chemstation, star worstation, Millenium 32

Hi Fabio, which kind of work do you want to do with these alternative SW's?

At least I will need to adjust mass spectra for report... graph overlay, labeling peaks, axis adjustments... etc

Proteowizard is pretty powerful when it comes to converting formats that free tools understand (e.g. you'll probably want to store mzML these days).

Then you can proceed with OpenMS, especially TOPPAS (a graphical workflow manager) to drag'n drop the workflow you need (very powerful tools in there, but you'll probably need to work though some of the tutorials).

Hi.

I use the DataAnalysis 3.4 version for Bruker HCT ultra.

For mass spec and under data Analysis, I usually chose "export", then "mass spectrum" and save it as "Simple x-y ASCII File (*.xy)". Then you can use excel, origin or other software to set up your spectra.

For LC traces the better I found is the following: I convert (using the export option) the files into "Agilent ChemStation File" and then convert (we also have Agilent Chem station software) the lc-ms trace into a CSV file than can then be used by excel.

To use open source software you will need some software to convert your files to an open file format such as mzXML and proteowizard should do that. Once you have that you could use the trans proteome pipeline (TPP) (http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP) which has good tutorials and a google discussion forum where you can place questions and people try to answer them. You can aslo do good searches using the global proteome machine (www.thegpm.org). Hope this helps

Thank you all for the replies. I will take a look at those suggestions. I am also using mMass that I find very decente - specially in the Windows version that can be linked with the spectra conversion tool from Bruker.

OpenChrom is an open source software for the analysis and visualization of mass spectrometric and chromatographic data.

https://www.openchrom.net/

The aim of OpenChrom is to support a wide range of different data formats natively. The appropriate vendor converters can be installed from the OpenChrom marketplace. Their usage is free of charge. Moreover, OpenChrom supports several open formats to save the analysis results.

In addition, OpenChrom offers its own open source format (*.ocb) that makes it possible to save the edited chromatogram as well as the peaks and identification results.

http://en.wikipedia.org/wiki/List_of_mass_spectrometry_software

What type of data is it? small molecule or peptides? For peptides EBI have lots of free tools particularly for peptide ID such as peptide shaker. Also go to

http://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList

This is a fairly comprehensive list of what is out there

I face same problem to export the data from UNIFI software to Masslynx or another software.

Hi,

I think this resource may be useful for you https://www.openms.de/

There is a MS data viewer at

http://msxpertsuite.org/screenshots/minexpert/features-page/minexpert-features.html

that is called mineXpert. Free software that allows mining MS1 data and ion mobility MS data. Linux/Mac/Win.

Hi, brother. Do you have find the appropriate software?

The latest mineXpert2 version can load mzML files, then provide you with a large set of methods to visualize your data and to mine them through MSn capabilities.

See that manual here:

http://msxpertsuite.org/user-manuals/html/minexpert2-user-manual/index.html

Thank you very much！

Hello Everyone, Where can I get the Compass DataAnalysis software setup and log in credentials. I desperately need it to analyze my Mass spectra.

Thank you

Thanks

The Compass DataAnalysis software is proprietary software by Bruker. It is *not* freely available! If you want to analyze data without shelling out thousands of dollars, then you first need to convert your raw data files to an open standard fomat (typically mzML, as wrote Chris Bielow above) using the ProteoWizard msConvert program. Then, the data are readable by a wealth of pretty good software (typically real Free Software, most often from highly recognized scientists in their field).

Some projects:

OpenMS

pyMzML

ProteoWizard

mzMine2 (does not handle ion mobility MS)

and finally

mineXpert2 (software by Filippo Rusconi at msxpertsuite.org)

...

Happy data visualization and exploration !

You can use Mestrenova. It's free and allows complex analysis as well.

OnenMS is a freeware that can be used.