Use of a Label-Free Quantitative Platform Based on MS/MS Average TIC to Calculate Dynamics of Protein Complexes in Insulin Signaling |
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| Authors: | Xuemei Yang Adam Friedman Shailender Nagpal Norbert Perrimon John M. Asara |
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| Affiliation: | 1.Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215; ;2.Harvard Medical School, Boston, Massachusetts 02115; and ;3.Innovagene Informatics, Framingham, Massachusetts 02143 |
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| Abstract: | A label-free quantification strategy including the development of in-house software (NakedQuant) to calculate the average TIC across all spectral counts in tandem affinity purification (TAP)-tagging liquid chromatography-mass spectrometry MS/MS (LC/MS/MS) experiments was applied to a large-scale study of protein complexes in the MAPK portion of the insulin signaling pathway from Drosophila cells. Dynamics were calculated under basal and stimulating conditions as fold changes. These experiments were performed in the context of a core service model with the user performing the TAP immunoprecipitation and the MS core performing the MS and informatics stops. The MS strategy showed excellent coverage of known components in addition to potentially novel interactions. |
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| Keywords: | LC/MS/MS, quantification, proteomics, signal transduction, average TIC, spectral counting, protein– protein interaction, networks |
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