Should I remove runs that have been imported with warnings?

Data problems that don't prevent the run being imported will result in a warning status. If this happens, the run's ion map will be shown with a yellow outline in the list of imported runs. When selected, a list of warnings is shown in a yellow box at the right on the main ion map:

The yellow outline and warning icon on an imported run that has warnings

An example of the warning messages shown when the run is selected

Warning messages

Some examples of messages you may see are:

"1328 scans after scan 3600 were ignored because they had lower retention times."

In our experience, this is typically caused by one of the following two situations:

The run file actually contains data for multiple runs
If you're not confident that each run in the file covers the same retention time range, then it's probably best to remove the run from the experiment. This is because, otherwise, you could end up with the tail end of a later run appended to the whole of the first run in the file. Conversely, if you're confident the ion map shows only a single run, it may be ok to keep the run in the experiment.
The run file has been created using a non-standard representation of retetion time
This situation appears to arise from the use of some third party tools that convert vendor-specific file formats into mzXML.

"Some m/z-intensity pairs were skipped because the m/z values were lower than preceding pairs."

This is known to occur with some files generated from Orbitrap Elite machines. The warning message appears if some m/z values within a scan are slightly lower than preceding values. In this case the points with lower m/z values are skipped.

In this situation, it is unlikely that you would need to remove the run from your experiment, but it may be worth contacting your Thermo representative for further advice.

"The background processing required for MSe identification is incomplete, but the raw data folder is missing - MSe identification will be unavailable until you restore the raw data and re-open the experiment."

This occurs when you have imported runs into an experiment with MSᴱ data, but the raw data folder was moved before the processing of the MSᴱ data could take place.

You can continue with the warning, but any MSᴱ data will be unavailable for peptide identification. It is recommended that you move the raw data back to its original location and then close and reopen the experiment to make use of the MSᴱ data.

"Function 3 has an empty drift time (.cdt) file, treating this function as non-drift time."

This warning occurs for Waters data when a function in the data folder was expected to contain drift time data, but the drift time (.cdt) file was empty.

If you didn't expect the data folder to contain drift time data, you can safely ignore this warning.

If, however, you did expect drift time data to be loaded, this run should be removed, and you should investigate why the drift time file is empty. This could be due to an incomplete copy of the data being made, or it could be an issue with data collection.

If this happens regularly, we recommend contacting your Waters representative.

"Unable to perform mass calibration for function 3. No calibration has been applied to this function."

This warning occurs for Waters data when calibration data is missing or invalid, so your data will be left uncalibrated.

  • The _HEADER.TXT file is missing from the raw data folder.
  • No calibration parameters were found in the header file for the given function.
  • Too few calibration parameters were found in the header file for the given function.
  • A calibration parameter is too large or incorrectly formatted.
  • No calibration type was present for the given function.

If your calibration has not been carried out externally, we recommend removing the run and checking that the raw data folder is in tact and has not been modified since being created (specifically the _HEADER.txt file).

Again, if this happens regularly, you should contact your Waters representative.

See also