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
Some Nice Videos from the MaxQant folks here