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Progenesis QI for proteomics

The next generation in LC-MS proteomics data analysis software.
Discover the significantly changing proteins in your samples.

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How can I assess the quality of my runs in the Import Data screen?

When importing your runs, Progenesis may encounter problems with the data that can affect your analysis. Some of these problems are more severe than others, but how do you judge whether they're severe enough to warrant removing the run from the experiment?

1. Check the import results

There are 3 possible results when importing a run; these can be seen in the list of runs at the left of the Import Data screen, when the Import details view is selected (show me).

Failed to import
The data in the run could not imported at all. You can safely remove the run from the experiment, as it cannot contribute further to your analysis.
Imported with warnings
Runs imported with warnings may still be usable for analysis. If you decide to keep these runs, you should still review their chromatography (see below).
Imported successfully
Runs that have been imported successfully should still be reviewed for chromatography problems; the successful import simply means the file has the expected format.

2. Reviewing the chromatography

Even when a run passes all of the automatic QC checks during import, it is still recommended to review its ion intensity map. There may be more subtle problems with its chromatography that are more easily spotted by eye.

For further information and advice on the types of problems you might see and how they will appear in the ion map, see the following article:

Blog: 5 sample-running problems highlighted by ion intensity maps

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