Third pass annotation

If the first two annotations are not successful we now do a third pass annotation which is only available for data file (it's an internal structure) based result's like TXT and XLS files.
At this point we load the rawdata files (netcdf format) and find the average retention time for the current bin with a missing value and use the intensity for the quantification ion - the noise in this area for this ion.

The average retention time is calculated using all samples with this bin of the day where the missing value is.  The noise is based on the minimum intensity of the given ion in the current sample in a specified retention index window.

You need to define this algorithm in an sop if you would to use it, since it's not enabled by default. This is related to the fact that you need to generate the netcdf files and store them on a directory which can be accessed by the application server. It is also a pretty slow process and can take up to several minutes for each sample.

To save storage place on your harddrive you can compress the netcdf files using the gzip algorithm and the software is smart enough to detect this and unpack these files in the memory.