mzML files

Finnee2016 only works with mzML file format.

How to convert proprietary files to mzML

Various software, most freely available, allow converting proprietary files to mzML. The HUPO keeps a list of available [software and freeware] (http://psidev.info/mzml_1_0_0%20). In most cases, msConvert from ProteoWizard will do the job perfectly.

Converting to mzML using msConvert

1. download and install ProtopWizard from [here] (http://proteowizard.sourceforge.net/downloads.shtml) carefully following every step.
2. start msConvert
3. After loading your file and having selected the output directory, un msConvert using all basic options and either without any filters selected ([profile spectrum format] ( https://github.com/glerny/Finnee2016/wiki/Profile vs centroid spectrum)) or only Peak Picking ([centroid spectrum format] ( https://github.com/glerny/Finnee2016/wiki/Profile vs centroid spectrum)). Finnee2016 is not aimed at MSn applications.
   

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] (https://www.bruker.com/service/support-upgrades/software-downloads/mass-spectrometry.html). IonSource made a detailed [tutorial] (http://www.ionsource.com/functional_reviews/CompassXport/CompassXport.htm). 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 (guillaume@fe.up.pt), 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 in 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] (https://data.mendeley.com/datasets/cb4hv9cp2c/2)

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Next         : [Converting an mzML file to a Matlab object] (https://github.com/glerny/Finnee2016/wiki/Converting-an-mzML-file-to-a-Matlab-object)
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