Picky: a simple method designer for targeted proteomics

Targeted proteomic approaches like selected reaction monitoring (SRM) and parallel reaction monitoring (PRM) are increasingly popular because they enable sensitive and rapid analysis of a preselected set of proteins. However, developing targeted assays is tedious and requires the selection, synthesis and mass spectrometric analysis of candidate peptides before the actual samples can be analyzed. The SRMatlas and ProteomeTools projects recently published fragmentation spectra of synthetic peptides covering the entire human proteome. These datasets provide very valuable resources. However, extracting the relevant data for selected proteins of interest is not straightforward. For example, developing scheduled acquisition methods (i.e. analyzing specific peptides in defined elution time windows) is complicated and requires adjustments to specific chromatographic conditions employed. Here, we present Picky: a fast and easy to use online tool to design scheduled PRM/SRM assays (https://picky.mdc-berlin.de). Picky (i) automatically generates optimized and scheduled SRM/PRM assays for proteins of interest and (ii) provides means to validate the data via known fragmentation spectra of corresponding synthetic peptides.