Maximizing proteomic information from MS data: Enhancements to Protein Prospector, a suite of programs for mining genomic databases

Protein Prospector is a suite of tools to interrogate genomic databases that is freely available via the UCSF Mass Spectrometry Facility website. Since its inception in 1995 it has continually improved in both breadth and functionality. Here we document enhancements and additions to the next public release and we describe current research on the development of several new tools. It is a selection of CGI programs written in C++ with an HTML interface. It can be served from either Windows NT or Sun Solaris webservers. All of the computational work was carried out within this web server framework. MALDI peptide mass maps were obtained from a Voyager DE STR reflectron TOF mass spectrometer (PE Biosystems, Framingham). MS/MS data came from a PE Sciex QSTAR (PE Sciex, Concord, Ontario) equipped with a nano ElectroSpray source (Protana, Odense). Nanoflow LC was performed with an LCPackings Ultimate chromatography system flowing at 250 nanoliters/minute with an LC-Packings 75 micron diameter C18 PepMap column. The gradient used was 5% B to 50 % B in 30 minutes where Solvent A was water with 0.05 % formic acid and Solvent B was acetonitrile with 0.04 % formic acid. For LCMS the Ultimate HPLC was coupled to the PESciex QSTAR mass spectrometer equipped with a Sciex MicroIonSpray source.