Percolator
Retention time and calibration information
Percolator provides a possibility to use so called description of correct features, i.e. features for which desirable values are learnt from the previously identified target PSMs. The absolute value of the difference between desired value and observed value is the used as predictive features. Percolator currently implements the description of correct features retention time, calibration and iso-electric point.
The option for using these features is -D and a specification of which features we would like to use – specified by a number given by adding up:
| 1 | iso-electric point |
| 2 | mass calibration |
| 4 | retention time |
| 8 | delta_retention_time*delta_mass_calibration |
If we are using retention time features we should specify a file containing the observed retention times using the
-2 option (otherwise scan numbers are used as proxies for retention time). So if we want to use all features except for the iso electric point calculation feature (this is the recomended usage) we should specify$ percolator -D 14 -2 my.mzXML -E pin.xml -X pout.xml.
If tab delimited input is used (the -j option) the retention time and mass difference should e specified in the third and forth column of the tab delimited file. In such case there is no need to give a separate retention time providing file with the -2 option.