protein, stP bias

Syntax

The parameter can have the values yes or no.

Notes

1. Default value = yes.
2. Introduced in version 2010.01.01.1.

Description

Assigning phosphorylation sites to sequences identified from tandem mass spectra can be challenging. Often there is little evidence for assigning one phosphorylation site versus another. For example, the following two interpretations may be equivalent in terms of the underlying MS/MS data:

1. AGGPTtPLSPTR
2. AGGPtTPLSPTR

where the phosphorylated residue is indicated by the lower case "t". However, it is known that the motif [ST]P corresponds to a very common type of kinase specificity. When this parameter is set to yes, phosphorylations that correspond to the motif [ST]P are given a very small (0.1%) scoring advantage over all other phosphorylated models. This advantage is small enough that any signal in a spectrum that could be used to choose one model over another will produce a much larger increase in score than this bias.

Another common case in phosphorylation analysis is attempting to distingish between model solutions such as:

1. AySFCGTVEYMAPEVVNR
2. AYsFCGTVEYMAPEVVNR

in which there is the potential for the phosphorylation to occur on a tyrosine or a nearby serine (or threonine). When this parameter is set to yes, models containing phosphorylated serine or threonine that have a pronounced peak (relative intensity > 20) corresponding to the neutral loss of phosphoric acid (H₃PO₄, -98 Da) are given additional scoring weight. The additional weight is significantly less than would be added for a sequence-specific ion, but it may be sufficient to distinguish between two solutions of the type shown above.