enviMass

enviMass requires your measurement files to be in the open .mzXML data format and to be centroided. Although the different vendors have different formats for their mass spectrometric acquisition files, these vendor-specific formats can be converted into .mzXML using either vendor-provided tools or the freely available msconvert tool. The latter tool can be downloaded from → ProteoWizard and then installed. Otherwise, contact your LC-MS instrument vendor.

Having installed MSConvert, you may use it via command-line or through its GUI, as described here. Four settings in the msconvert GUI are to be included for file conversion to the centroided .mzXML format, cp. points (A) to (D) in the GUI screenshot:

1. Select your LC-MS acquisition files (e.g., .wiff, wiff2 or .raw formats) press the Add button to include them into your file selection.
2. Specify the output directory into which the .mzXML files are to be written. Select mzXML as output format and the encoding precisions (it is recommended to run enviMass with 64bit Windows).
3. One filter must be included to perform a centroidization of the profile data in each scan. This filter is called peakPicking (not to be confused with the enviMass peak picking from the extracted chromatograms) and can be selected from the Filters drop-down selection.
   Do not forget to press the Add button to include this filter during file conversion.
4. Start the conversion process; this may take some time.

In additon, Thermo .raw files can be read directly by enviMass when having the MSConvert tool installed. To do so, users must register the path to msconvert.exe in each of your projects, as described in the → loading files, File formats section.

Conversion of Waters file formats to centroided .mzXML seems slightly less straightforward, but has been achieved by some enviMass users. One reported approach (for a Synapt G2-S HDMS or similar) is:

1. Using → Waters MassLynx software, run a (lock-mass correction and) file centroidization with the automatic peak detection option (here, peak detection refers to centroidization).
2. Manually delete the lock-mass functions (three _FUNC003 files .DAT, .IDX, .STS) in each resulting data folder. It is not yet clear if this step is always compulsory.
3. Finally convert these files to the .mzXML file format using either of
   
   
   • → ProteoWizard MSConvert (with Filters → Threshold Peak Filter → Threshold type: Count, Orientation: Most intense, Value: 500(?) → Add; compare also to the steps A, B and D (not C!) described above for Sciex, Thermo or Agilent formats),
   • → massWOLF (options --mzXML --MSe) or
   • → X2XML (options unknown).

You may upload the resulting .mzXML files into enviMass (should not take ages for each file after approriate filtering), run the peak picking step only (i.e., disable all steps in the enviMass Workflow tab, press the Apply and then the Calculate button), move to the Data viewer tab once the calculation has finished and select a file to view its centroid data points plus any peaks picked from them. Namely, after (a) having enabled the visualization of raw data centroids and (b) having zoomed far enough into an RT and/or m/z range to see the individual centroid points (gray and red dots), is there any strong mass discretization over RT visible between centoids adjacent in mass? There shouldn`t be any. Are any of the centroid data points highlighted in red, indicating that peaks of reasonable chromatographic shape have been picked? There should be at least some ...

Updates on any alternative or additional approaches are welcome and might help other Waters users. Conversion approach provided without any warranty.