Did you know the Proteomics core and the Bioinformatics core here at the Genome Center can help you analyze your data using the newest data analysis tools.
A good example is using the SAINT tools to analyze your AP (Affinity Purification) results. SAINT allows you to calculate probabilities that your interacting proteins are true interactors vs non-specific binding proteins. These tools requires a certain number of negative control experiments be performed, so please let us know if you want to give it a try
In addition, we are working on bringing you advanced analysis of Label free intensity data using QPROT and MSstats. Both offer advanced statistical modeling to discover differentially expressed proteins