MudPIT Simulator

Multi-dimensional Protein Identification Technology (MudPIT) is a shotgun proteomics technique capable of identifying thousands of proteins in proteolytically digested complex mixtures. This strategy was developed in the Yates lab. Similarly to traditional two-dimensional gel electrophoresis, MudPIT separates peptides according to two independent physicochemical properties but uses two-dimensional liquid chromatography (LC/LC) online with the ion source of a mass spectrometer.  This separation relies on columns of strong cation exchange (SCX) and reversed phase (RP) material, back to back, inside fused silica capillaries. The chromatography proceeds in cycles where each consists in increasing salt concentration to free packets of peptides off the SCX followed by a hydrophobic gradient to progressively elute peptides from the RP into the ion source.  This process identifies mixture components by tandem mass spectrometry (MS/MS).  Since PatternLab is devoted to shotgun proteomic data, we present an interactive MudPIT simulator for didatic purposes. Its interface is demonstrated below and it can be installed in you computer through this link. The software will automaticaly search for updates in this site from time to time.

This sim is a simplification of reality; therefore the timescale and many other features are not faithful representations.  The green and pinkish structures in the upper part of the simulator represent the strong cation exchange and the reverse phase material packed in the capillary (yellow structure).  The semi-conical structure represents the mass spectrometer nozzle (entrance) and the structure below is an X-Ray of a quadrupole ion trap. The artwork of the ion trap is a modified version of that obtained from Thermo.