iPhos: a web tool to streamline the alkaline phosphatase-assisted LC-MS phosphoproteome investigation

Abstract

iPhos is a web based software toolkit to facilitate and streamline the work-flow of the alkaline phosphatase-assisted phosphoproteome characterization Comprehensive characterization of the phosphoproteome in living cells is critical in signal transduction research But the low abundance of phosphopeptides among the total proteome in cells remains a challenge in mass spectrometry-based proteomic analysis To overcome the obstacles an alternative analytic strategy to confidently identify phosphorylated peptides by using the alkaline phosphatase (AP) treatment in combination with high-resolution mass spectrometry was provided by Liao’s group While the process is applicable the key integration along the pipeline was mostly done by tedious manual work In order to be effective and convenient iPhos not only has a user friendly web interface but also assists the experiment work-flow in data analysis We further demonstrated the utility of the iPhos toolkit on the data of human metastatic lung cancer cells (CL1-5) In the comparison study of the control group of CL1-5 cell lysates and the treatment group of dasatinib-treated CL1-5 cell lysates we demonstrated the applicability of the iPhos toolkit and reported the experimental results based on the iPhos-facilitated phosphoproteome investigation Additionally we also compared the strategy with pure DDAbased LC-MS/MS phosphoproteome investigation The results of iPhos-facilitated targeted LC-MS/MS analysis convey more thorough and confident phosphopeptide identification than the results of pure DDA-based analysis The iPhos software toolkit and sample tutorial data are available online at http://cosbi3 ee ncku edu tw/iPhos/

Date of Award	2015 Jun 8
Original language	English
Supervisor	Wei-Sheng Wu (Supervisor)