Abstract
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 that we distribute freely to the scientific community at ProHitsMS.com, and which is under continuous development. The complete ProHits solution1 performs scheduled backup of mass spectrometry data and initiates database searches (Mascot, X!Tandem, COMET, SEQUEST and the output from the TransProteomics Pipeline are now supported). It stores search results and enables linking the mass spectrometry data to entries in the relational database module called “Analyst”, which is also available as a stand-alone application (including as an easy-to-install virtual machine implementation2). ProHits Analyst is organized in a hierarchical manner by project, bait, experiment and sample and also serves as an electronic notebook. When a sample is created, mass spectrometry search results can be uploaded. Search results can be explored using a series of viewers, filtered based on mass spectrometry quality, frequency of detection or background lists, viewed in Cytoscape-Web or exported to text or as a PSI XML format for deposition in interaction databases. Importantly, however, search results can be further analyzed using the SAINT statistical tool which is seamlessly integrated within ProHits to derive interaction confidence scores(3-5). With the integration with a number of open source tools and public repositories, ProHits facilitates transparent analysis and reporting of AP-MS data.
1PMID:20944583
2PMID:22948730
3PMID:20489023
4PMID:21131968
5PMID:22948729