Exploratory features in this version of the product include:

PeptideProphet discriminant function for X! Tandem

PeptideProphet scores calculated from runs that use native X!Tandem scoring using a discriminant function that has not been published or peer reviewed. Published results should always include the native X!Tandem scoring columns for the peptide-level results.

Hydrophobicity peptide column

The hydrophobicity peptide column implements version 3.0 of the Oleg Krokhin retention time prediction algorithm. Version 1.0 of the Krokhin algorithm has been published (An Improved Model for Prediction of Retention Times of Tryptic Peptides in Ion Pair Reversed-phase HPLC, Krokhin, et al), but version 3.0 has not.

DeltaScan peptide column

This score is an attempt to measure the deviance between actual and predicted retention time. For each fraction, we first attempt to correlate hydrophobicity (this is calculated using the algorithm published by Oleg Krokhin, et al) with scan numbers by calculating a linear regression between scan and H for all peptides in the fraction with PeptideProphet score greater than 0.99. These coefficients are stored with the fraction and used to calculate a theorhetical scan number for all peptides in the fraction. The DeltaScan value expresses, in standard deviations, how far a particular peptide's scan number is from the predicted value.