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.
MS/MS database search info:
- Search engine comparisons: link1,
link3 (only OMSSA searched 3+ spectra!),
- 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
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:
- Evaluation of peak count filtering (the "minimum_peaks" parameter in UWPR SEQUEST)
Software tools and protocols from other resources: