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MassLynx overwrote my samples without warning - WKB2358

Article number: 2358


  • Accidentally queued up a batch of samples in which one of the file names was exactly the same as a file name from the previous batch in the sample list
  • MassLynx did not warn that the file already exists
  • MassLynx did not ask if intent was to overwrite the file
  • Original file was overwritten by the second sample's information, without warning or error message



  • MassLynx
  • Sample list


MassLynx always determines if file names already exist in a project before accepting any batch into the queue.

File names of samples in a queue waiting to be run do not yet exist as a file name (*.raw folder), which is created at the end of a sample's run, immediately prior to executing the sample analysis process.

MassLynx checks for duplicate file names only at batch submission, with the option to cancel the batch (unless MassLynx Security is running).


  1. Manually check that the file names are unique before submitting to sample queue.
  2. Submit second batches into a different project.
  3. Use MassLynx Security, in which case the user is not granted overwrite permission and the acquisition stops the queue without analyzing the sample that has the duplicate file name.



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