A tool with a graphical interface that performs various tasks including
creating mgf files, running Hardklör, merging HCD/CID scans for iTRAQ analysis,
calculating precursor contamination for iTRAQ data, etc.
Various MS/MS database search tools are available at our UWPR systems.
Search tools (besides Mascot) are run on a cluster composed of over twenty 8-core nodes, each with 16GB RAM.
Search results are typically processed through the Trans-Proteomic Pipeline.
RawMeat is a nice Thermo raw file diagnostic
tool developed by the now defunct Vast Scientific. RawMeat requires Thermo's MSFileReader library
to be installed. MSFileReader can be downloaded by creating an account with
Once registered you will find the software under "Other Software Releases".
Be wary of multiple-stage searches like X!Tandem's refinement mode or the hot-spot
searching that Paragon does. Not that these searches are innately bad but rather one should be
educated on the search strategy and what it means. If one searches a bazillion spectra against
subset proteins X, Y, and Z in the 2nd pass, don't be surprised to find many matches
(real or spurrious) to proteins X, Y and Z. Think of it as a self-fulfulling prophecy.
Here's an interesting paper and follow-up touching on the problem and proposing solutions
to the target-decoy strategy with these types of searches: