mzML files

Finnee2016 only works with X-HRMS files in mzML format. This format has been developed by the Human Proteome Organization (HUPO) and allows converting proprietary MS files to an XML-likes format that can easily be processed.

How to convert proprietary files to mzML

Various software, many freely available, allow converting proprietary data to mzML. The HUPO keeps a list of available software and freeware. While msConvert can usually convert any proprietary formats, we encounter some problems with Bruker baf files. For those, CompassXport seems better.

Converting to mzML using msConvert

1. download and install ProteoWizard from here carefully following every step.
2. start msConvert.
3. After loading your file and having selected the output directory, run msConvert using all basic options and either without any filters selected (profile format) or only Peak Picking (centroid format). Finnee2016 is not aimed at MSⁿ applications, and we recomand not using any filters to record the MS spectra as profile.

Converting to mzML using compassXport

compassXport is the freeware from Bruker that allows converting Bruker proprietary .baf files to various open formats including mzML. While registration in the Bruker site is required, the software is free and can be downloaded here. IonSource made a detailed tutorial. CompassXport can also be run from Matlab using the script below (you can copy/paste but don't forget to change the path).

    function status = runCompassXport(type)  
    %% DESCRIPTION  
    % 1. DESCRIPTION RUNCOMPASSXPORT is used to run the software  
    % CompassXport(tm) that allows to convert a file recorded by a mass   
    % spectrometer from Bruker to a mzML file. type should either be 'centroid'  
    % or 'profile'. Please visit https://finneeblog.wordpress.com/ for more  
    % information  
    %   
    % 2. COPYRIGHT  
    % Copyright 2016-2017 G. Erny ([email protected]), FEUP, Porto, Portugal  
    
    % path2CompassXport should be modify to be your path to CompassXport  
    path2CompassXport = 'C:\Program Files (x86)\Bruker Daltonik\CompassXport\CompassXport.exe';   
    
    [fileName, pathName] = uigetfile(cd, 'Select the Bruker baf file', '*.baf');  
    targetFile = fullfile(pathName, fileName);    
    [pathstr,name,~] = fileparts(targetFile);  
    nameList = strsplit(pathstr, filesep);   
    [~, name, ~] = fileparts(nameList{end});    
    NewName = fullfile(pathstr, [name, '.mzML']);    
    [fileName, pathName] = uiputfile('*.mzML', 'Enter the new name for the mzML file', NewName);   
    destinationFile = fullfile(pathName, fileName);  

    switch type
      case 'centroid'
        command = ['"' path2CompassXport  '"' ' -a ' '"' targetFile '"' ...
            ' -o ' '"' destinationFile '"' ' -mode 2' ' -raw 0'];
        % the mode # allows to specify the format. 0: mzXML, 1: mzData, 3:
        % mzML, 4: CSV. raw allow to specify the 'spectrum type'. raw 0 for 
        % 'centroid (line) spectrum' type and raw 1 for 'profile spctrum'
        % type. It should be noted that centroid spectrum are not
        % calculated by CompassXport but by the Bruker acquisition software 
        % (usually and 
        % stored in the .baf file.  
        
      case 'profile'
          command = ['"' path2CompassXport  '"' ' -a ' '"' targetFile '"' ...
              ' -o ' '"' destinationFile '"' ' -mode 2' ' -raw 1'];
      otherwise
          error('only ''centroid'' and ''profile'' are recognised as spectrum type');   
    end

    status = system(command);
    end

With the acquisition software

Some modern software allows exporting data in mzML format. Check your manual for this option.

Repositories of files

mzML files can be obtained online

• CE-TOFMS data from a urine sample - mzML files with scans in profile or centroid spectrum format
• UHPLC-QTOFMS data from a urine sample - mzML files with scans in profile or centroid spectrum format

Remarks on MS instrument setup

At the moment, when starting Finnee only MS¹ scans are recorded, in future releases MSⁿ data will also be used. However, from our experience, better results are obtained if the MS instrument is set up for MS¹ experiment, this because the scan rate is constant allowing a better estimation of the background noise. Similarly, low-intensity points should not be filtered out; those are needed for the determination of the background noise.

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Previous: How to install Finnee2016

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