PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data.

Background: We have created a software implementation of a published and verified method for assigning probabilities to potential phosphorylation sites on peptides using mass spectrometric data. Our tool, named PhosCalc, determines the number of possible phosphorylation sites and calculates the theoretical masses for the b and y fragment ions of a user-provided peptide sequence. A corresponding user-provided mass spectrum is examined to determine which putative b and y ions have support in the spectrum and a probability score is calculated for each combination of phosphorylation sites.

Considerations on post-translational modification and protein targeting in the Arabidopsis defense proteome.

The immune response of plants to potential pathogens consists of two levels of defense; basal resistance triggered by pattern recognition (PTI) and effector triggered immunity (ETI). Recent analysis of the Arabidopsis proteome after challenge by three strains of Pseudomonas syringae identified proteins implicated in the establishment of disease, PTI and ETI. In this addendum we discuss the significance of some of the putative post-translational modifications and the predicted localisation of these proteins.