Filtering quantification data with average reporter ion signal-to-noise values - Proteome Discoverer Software - Filtering quantification data with average reporter ion signal-to-noise values - Proteome Discoverer Software - Proteome Discoverer Software

For Orbitrap data, you can obtain more reliable TMT quantification results by filtering out quantification spectra with too few ions for the reporter ion signals. The Reporter Ions Quantifier node includes a parameter, Average Reporter S/N Threshold, that you can use to specify an average reporter S/N threshold value that determines which PSMs the application excludes from quantification. The application filters quantification values by excluding PSMs that have an average reporter ion S/N value smaller than this threshold value.

In addition, the Average Reporter S/N threshold parameter adds the Average Reporter S/N column, which displays average reporter ion S/N values on the PSMs and Quan Spectra pages. The application calculates the values as the sum of S/N values found, divided by the number of defined tags.

In the following example, the application calculates the average S/N values for a result file created from an MSF file containing TMT 6plex data. The quantification method has six channels, and the application calculates the average S/N value by sum(S/N) divided by 6. The following table shows the results.

In the following example, the application calculates the average S/N values for a result file created from two MSF files containing TMT 6plex data. The quantification method for both files has six channels, and the application calculates the average S/N by sum (S/N) divided by 6. The following table shows the results.

When you combine MSF files containing reporter ion quantification data with MSF files lacking reporter ion quantification data, the PSMs without reporter ion quantification data display no values in the Average Reporter S/N column on the PSMs and Quan Spectra pages.