UNIT 8.16 Using ProHits to Store, Annotate, and Analyze Affinity Purification–Mass Spectrometry (AP-MS) Data
Published Online: 1 SEP 2012
Copyright © 2012 by John Wiley & Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
How to Cite
Liu, G., Zhang, J., Choi, H., Lambert, J.-P., Srikumar, T., Larsen, B., Nesvizhskii, A. I., Raught, B., Tyers, M. and Gingras, A.-C. 2012. Using ProHits to Store, Annotate, and Analyze Affinity Purification–Mass Spectrometry (AP-MS) Data. Current Protocols in Bioinformatics. 39:8.16:8.16.1–8.16.32.
- Published Online: 1 SEP 2012
Affinity purification coupled with mass spectrometry (AP-MS) is a robust technique used to identify protein-protein interactions. With recent improvements in sample preparation, and dramatic advances in MS instrumentation speed and sensitivity, this technique is becoming more widely used throughout the scientific community. To meet the needs of research groups both large and small, we have developed software solutions for tracking, scoring and analyzing AP-MS data. Here, we provide details for the installation and utilization of ProHits, a Laboratory Information Management System designed specifically for AP-MS interaction proteomics. This protocol explains: (i) how to install the complete ProHits system, including modules for the management of mass spectrometry files and the analysis of interaction data, and (ii) alternative options for the use of pre-existing search results in simpler versions of ProHits, including a virtual machine implementation of our ProHits Lite software. We also describe how to use the main features of the software to analyze AP-MS data. Curr. Protoc. Bioinform. 39:8.16.1-8.16.32. © 2012 by John Wiley & Sons, Inc.
- affinity purification coupled with mass spectrometry;
- data analysis;
- virtual machine;
- statistical models;
- protein-protein interactions