Data Analysis Tools

Online Tools/Calculators


Mass Spec Utils

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.

MS/MS database search tools

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.

Software tools and protocols from other resources:


MS/MS database search info:

  • Search engine comparisons: link1, link2, link3 (only OMSSA searched 3+ spectra!), link4, link5, link6
  • Be wary of searching with too narrow a precursor tolerance (even if your mass spectrometer can measure that accurately). It's an issue with all search tools. This paper nicely touches on the problem and here's a rebuttal.
  • 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: paper1, paper2