Supported file formats

 

File formats that can be directly uploaded to XCMS Online are:


Please do NOT upload .zip files !   The XCMS Online upload application will compress all files automatically during upload.
 

In future versions, additional formats will be directly supported by XCMS Online. In the meantime, file formats that are not supported yet should be converted prior to uploading them, using the converters shown in the table below. 

 

Vendor

Instrument Software

File Format

Converter

Can be uploaded
directly

Notes

SCIEX

Analyst

.wiff

ProteoWizard (see below)

YES

.wiff files can be uploaded directly and do not need to be converted manually. Please make sure the .wiff.scan files are uploaded together with the .wiff files.
Note for manual conversion: Conversion to centroid mode only works with most recent ProteoWizard versions (>= 3.0.3569)

Agilent

MassHunter

.d

ProteoWizard (see below)

YES

.d folders can be uploaded directly and do not need to be converted manually.
Note for manual conversion: A bug related to the conversion of Agilent was fixed recently, please update proteoWizard to newest version (>= 3.0.3782)

Agilent

ChemStation

.D

export from Chemstation as 'AIA'

NO

 

Bruker

Compass

.d, YEP, BAF, FID

CompassXport or

ProteoWizard (see below)

YES

.d folders can be uploaded directly and do not need to be converted manually.
1. to use the latest recalibration for the exported data a setting might need to be enabled in the windows registry (see CompassXport manual)
2. Only CompassXport 3.0.6 can convert data from the newest Bruker instruments at the moment.

Thermo Fisher

Xcalibur

RAW

ProteoWizard (see below)

YES

RAW files can be uploaded directly and do not need to be converted manually. Conversion of Q-Exactive data to centroid mode works only with most recent ProteoWizard versions  (>= 3.0.3631)

Waters

MassLynx

.raw

MassLynx (CDF)
ProteoWizard (see below)

YES

  1. .raw folders will be uploaded directly and do not need to be converted manually.
    If you get error messages like "Error in xcmsRaw(file, profstep = 0) : Time for scan XXX greater than scan YYY" you have to add the "sortByScanTime" filter for the file conversion as  described here.

  2. The exported data does not make use of the latest recalibration. No solution at the moment.

  3. Removing the lock mass calibration scans and filling in the resulting gaps in the data (Misc/Correct mass calibration gaps) seems to work only if files were converted to CDF format using MassLynx.



 

 

ProteoWizard Installation (For problems with proteoWizard usage, please contact proteoWizard developers directly.)


  1. Download ProteoWizard from http://proteowizard.sourceforge.net/downloads.shtml.   Important: choose the version “Windows (includes vendor reader support)”.
  2. Install ProteoWizard. You also must have  MSVC 2008 SP1 (x86).NET Framework 3.5 SP1 and 4.0 installed.
  3. From the Program menu, run  ProteoWizard -> MSconvert



 

ProteoWizard usage

We recommend converting files to mzXML in centroid mode, which saves upload time (smaller files) and will also make sure that the files are compatible with the centWave method for feature detection.

  1. From the Program menu, run  ProteoWizard -> MSconvert
    1. Click 'Browse' and select file(s) for conversion.
    2. Select mzXML as output format.
    3. Select 'Peak Picking' filter (centroidization) and click the 'Add' button.
    4. Start the conversion.