Data Analysis Tools

Online Calculators

CrossLinking

ProteinCenter
ProteinCenter by Proxeon (Thermo Scientific) is a tool that helps bridge the gap between raw data and biological insight. It is a great web-based tool for interpreting results from complex proteomics data sets.

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 results are typically processed through the Trans-Proteomic Pipeline.

Miscellaneous

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 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
  • Evaluation of peak count filtering (the "minimum_peaks" parameter in UWPR SEQUEST)

Software tools and protocols from other resources: