Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway.
Lian YiTujin ShiMarina A GritsenkoChi-Yuet X'avia ChanThomas L FillmoreBecky M HessAdam C SwensenTao LiuRichard D SmithH Steven WileyWei-Jun QianPublished in: Analytical chemistry (2018)
Large-scale phosphoproteomics with coverage of over 10,000 sites of phosphorylation have now been routinely achieved with advanced mass spectrometry (MS)-based workflows. However, accurate targeted MS-based quantification of phosphorylation dynamics, an important direction for gaining quantitative understanding of signaling pathways or networks, has been much less investigated. Herein, we report an assessment of the targeted workflow in the context of signal transduction pathways, using the epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) pathway as our model. A total of 43 phosphopeptides from the EGFR-MAPK pathway were selected for the study. The recovery and sensitivity of two commonly used enrichment methods, immobilized metal affinity chromatography (IMAC) and titanium oxide (TiO2), combined with selected reaction monitoring (SRM)-MS were evaluated. The recovery of phosphopeptides by IMAC and TiO2 enrichment was quantified to be 38 ± 5% and 58 ± 20%, respectively, based on internal standards. Moreover, both enrichment methods provided comparable sensitivity from 1 to 100 μg starting peptides. Robust quantification was consistently achieved for most targeted phosphopeptides when starting with 25-100 μg peptides. However, the numbers of quantified targets significantly dropped when peptide samples were in the 1-25 μg range. Finally, IMAC-SRM was applied to quantify signaling dynamics of EGFR-MAPK pathway in Hs578T cells following 10 ng/mL EGF treatment. The kinetics of phosphorylation clearly revealed early and late phases of phosphorylation, even for very low abundance proteins. These results demonstrate the feasibility of robust targeted quantification of phosphorylation dynamics for specific pathways, even starting with relatively small amounts of protein.
Keyphrases
- epidermal growth factor receptor
- mass spectrometry
- tyrosine kinase
- signaling pathway
- protein kinase
- small cell lung cancer
- cancer therapy
- advanced non small cell lung cancer
- pi k akt
- multiple sclerosis
- liquid chromatography
- capillary electrophoresis
- oxidative stress
- high resolution
- ms ms
- healthcare
- high performance liquid chromatography
- gas chromatography
- single cell
- amino acid
- high speed
- cell proliferation
- growth factor
- small molecule
- smoking cessation
- single molecule
- binding protein
- endoplasmic reticulum stress
- electronic health record
- wastewater treatment
- protein protein