Added by Vanessa Phelan, last edited by Mingxun Wang on Aug 07, 2017  (view change)

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Data Conversion - Easy

This is a complete package for Windows users to convert their vendor formats to GNPS compatible format (.mzXML). It is as easy as putting files into a folder and batch converting it all without any installation (well nearly so).

  1. Simply download the zip file here .
  2. Unzip contents onto a folder on your computer (e.g. Desktop)
  3. Install windows libraries in "pwizLibraries-and-Installation" - Run appropriate program for 32-bit (32-Bit_Double-Click_To_Install.bat) or 64-bit system (64-Bit_Double-Click_To_Install.bat). To find out which type of OS you have please check here
  4. Put vendor formats in "Input_Files" not embedded in other folders
  5. Double click on Double-Click_To-Convert.bit - Download zip includes demo files for major vendor formats as a test. 
  6. Wait patiently
  7. Check all files converted in Output_Folder
  8. If there are errors, please check log.txt or read on how to convert files in the detailed sections. 

This instructions should be able to handle Thermo, Bruker, Agilent, Sciex, and Waters DDA (data dependent acquisition) formatted data. 

Package has been tested to work with Windows 7 and Windows 10 64-bit. If you have another installation, definitely let us know at miw023@ucsd.edu what issues you are running into so we can make it better! Special shout out to Chase Clark for helping put this together. 

Caveats: With this package Bruker data will not utilize lock-mass and could result in a loss of pass accuracy. Please use other means to convert (described below) if this matters to you. 

Data Conversion - Detailed

For files to be operated on in the GNPS workflows, they must be in the correct format.  Only the following formats are acceptable: .mzXML, .mzML, and .mgf.

The .mzXML or .mzML format is strongly preferred and will be discussed in this tutorial for data conversion.

Vendor
Instrument Software
File Format
Converter
Notes
AB SCIEX
Analyst
.wiff
MSConvert
(see below)
has been verified
Agilent
MassHunter
.d
MSConvert
(see below)
has been verified (issue known with scan number export)
Bruker
DataAnalysis/Compass
.d
CompassXport
This conversion is through the DataAnalysis software and is detailed below.
ThermoFisher
Xcalibur
.RAW
MSConvert
(see below)
*verified
Waters
MassLynx
.raw
MSConvert
(see below)
*has not been verified

For problems with MSConvert, please contact the ProteoWizard developers directly: click here.

Inspecting the mzXML files

In order to verify conversion of the original data file to .mzXML, the openware Insilicos Viewer, or TOPP View (OpenMS) should be downloaded and installed. 

They can be downloaded here:

Insilicos

TOPP View (OpenMS)

If the .mzXML file you create does not open in the Insilicos or TOPP viewer, it has not been converted correctly.  Check to make sure you .mzXML data matches the data from your original files.

Conversion Using MSConvert

For problems with MSConvert, please contact the ProteoWizard developers directly: click here.

Download and install ProteoWizard from http://proteowizard.sourceforge.net/downloads.shtml

Important: make sure to choose the version Windows (includes vendor reader support). You must also have .NET Framework 3.5 SP1 and 4.0 installed.

After installation, from the Start Menu, click the ProteoWizard folder and open MSConvert.

Click Browse and select file(s) for conversion. Then Click Add to add them to the MSConvert workflow.

Choose an Output Directory

Under Options, choose mzXML for output format, 32-bit for binary encoding precision and uncheck Use zlib compression. Note that mzML files are also supported.

Under filters, choose Peak Picking with Vendor checked, in order to centroid the data. Indicate MS-Levels 1-2. Click Add to add the filter.

Click Start.  Check your folder for the new .mzXML files. Verify that these files open properly in Insilicos or TOPP View (OpenMS) http://www.openms.de/

Conversion of Bruker Data

If lockmass calibration is being used, make sure it is applied before conversion.

Conversion of Single Data File

To convert a single data file:

In DataAnalysis,

Under File, choose Export -> Chromatogram Analysis

Name your .mzXML file, choose mzXML for file type and Line Spectra

Click Save. Check your destination folder for the new .mzXML file.  Verify that this file opens properly in Insilicos.

Batch Conversion

Registry Edit Changes

Go into the regedit (registry edit) to modify the Registry Value to export 32 bit spectra:

Exporting Data as 32-bit

CompassXport (DataAnalysis uses CompassXport) will export to mzXML with two different precisions settings, 32- & 64-bit

Using Windows RegEdit,  locate

HKEY_CURRENT_USER\Software\Bruker Daltonik\CompassXport

 The precision is set

ExportPrecision64Bit : DWORD, selected export precision ( 0 = 32bit precision/float, 1 = 64bit precision/double)

 Registry Entry to set mzXML precision

 Key Name:         HKEY_CURRENT_USER\Software\Bruker Daltonik\CompassXport

Name:       ExportPrecision64Bit

Type:                REG_DWORD

Data:         0

 (this means 32bit will be exported)

Use Recalibrated Spectra

This Registry Entry should be fine, but check.

UseRecalibratedSpectra:

Export the latest recalibration of this analysis (1 = activated, 0 = deactivated).

(Should already be 1 or activated).

 Creating a Default Method for Batch Conversion

Create a default method:

In DataAnalysis, open any .d file. If you are using lockmass calibration, apply it.

Under Method -> Script

Type the following exactly as written:

option explicit
 
Dim Filename
 
' Clears existing compounds
 
Analysis.Compounds.Clear   
 
' Apply lockmass
 
Analysis.ApplyLockMassCalibration true  

' removes any existing results  
 
Analysis.ClearResults
 
'  save before export
 
Analysis.Save
 
'  export mzXML data
 
Filename = left(Analysis.path,len(Analysis.path)-2) & ".mzXML"

Analysis.Export Filename, daMzXML, daLine
 
Form.Close

Close script window.  Under method -> Save As...

Name and save your method under C:/Methods

With a .d file open, under Method -> Run.

This will apply this method to your open file.  If it is successful, you should have a new .mzXML file that will open in Insilicos with lockmass applied.

Applying Batch Conversion

After the default method is created, under Tools -> ProcessWithMethod

A new window will open.  Under Method choose the method that was created above.

Select data for conversion.

Click Process.

A ProcessQueue window will open.  Check to make sure that .mzXML files are being created. This will take up to several minutes per file depending upon the file size. Do not use DataAnalysis when this process is occurring.

The .mzXML files will be found in the same folder as the original data.  If successful, the new .mzXML files can be opened and viewed in Insilicos / TOPP viewer.

Single MS/MS Spectrum Conversion

This conversion is necessary to upload single MS/MS spectra to the libraries in GNPS.

In DataAnalysis, identify the scan number of the MS/MS spectrum you want to export.

The conversion will use MSConvert.  Follow the directions above to install ProteoWizard.

Browse for the original .d data file.

Choose an Output Directory

Under Options, choose mzXML for output format, 32-bit for binary encoding precision and uncheck Use zlib compression.

Under filters, choose PeakPicking with Prefer Vendor checked to centroid the data. Click Add to add the filter.

Under filters, choose Subset and type in the Scan Number you identified. Click Add to add the filter.

Click Start.  Check your folder for the new .mzXML files. Important! Rename the .mzXML file.

Verify that these files open properly in Insilicos or TOPP viewers