Quantification of Dynamic Protein Interactions and Phosphorylation in LPS Signaling Pathway by SWATH-MS

Abstract

The LPS-induced dynamic interactions and phosphorylation in MYD88, TRAF6, and NEMO complexes have been systematically mapped by SWATH-based quantitative proteomics. The results reported reveal highly dynamic complex assembly and complex regulation network in LPS signaling pathway.

Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line

“…A cross-comparison of publicly available datasets shows that many LPS-regulated proteins in different cell types and conditions exhibit the same trend in our time-course quantitative abundance dataset (Supplementary Data 10) as well as in the hyperLOPIT list of translocating proteins (Supplementary Data 9), thereby validating many of our findings presented here. A number of previous studies have utilised various proteomics approaches to explore the LPS-induced innate immune response in macrophages 9,10,82,83 , as well as to characterise individual subcellular organelles following LPS activation 11,12 . This study presents a global analysis to simultaneously track thousands of native proteins in response to LPS with a spatial context.…”

Generation of a murine SWATH-MS spectral library to quantify more than 11,000 proteins

“…Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra (SWATH-MS) is one of the DIA methods that has been employed to produce highly reproducible and complete quantitative results [1][2][3] . This property of SWATH-MS enables the general application of SWATH-based quantitative proteomics in biological research and clinical biomarker studies [4][5][6] . SWATH-MS data analysis can be accomplished by two strategies, spectral library-based targeted analysis approach and library-free analysis method.…”

“…The variable windows of SWATH-MS were "399.5-409.9, 408.9-418.9, 417.9-427. 4 Bioinformatics analysis. Building the murine spectral library.…”

“…Targeted analysis of SWATH-MS data using OpenSWATH-PyProphet-TRIC workflow. The workflow was performed as previously described 4 . SWATH-MS files were converted to 32-bit profile mzXML files using msconvert (Proteowizard V.3.0.447).…”

“…Protein quantification. Protein quantification was conducted as previously described 4 . The TRIC results were used for protein inference and quantification.…”