Two AP-SWATH protein interaction papers in Nature Methods

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Doug
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Two AP-SWATH protein interaction papers in Nature Methods

Postby Doug » Mon Oct 28, 2013 11:55 am

There are two papers in Nature Methods describing the use of Affinity Purification (AP) and SWATH technology (jointly called AP-SWATH) to quantitatively compare protein-protein interactions across samples. These caught my eye because in addition to PTM analysis I consider protein-protein interaction studies one of the most valuable uses of mass spectrometers in proteomics research. Both papers apply the method to a different biological system. One describes an AP-SWATH pipeline for data analysis but I am not sure whether or not they made that pipeline publicly available.

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system
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Sniper
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Postby Sniper » Sat Nov 02, 2013 7:56 pm

Doug wrote:There are two papers in Nature Methods describing the use of Affinity Purification (AP) and SWATH technology (jointly called AP-SWATH) to quantitatively compare protein-protein interactions across samples. These caught my eye because in addition to PTM analysis I consider protein-protein interaction studies one of the most valuable uses of mass spectrometers in proteomics research. Both papers apply the method to a different biological system. One describes an AP-SWATH pipeline for data analysis but I am not sure whether or not they made that pipeline publicly available.

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system


The AP-SWATH method is Highly dependent on the background information. if using SWATH to identify high throughput protein-protein interactions, that might not a application.


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