Data Analysis Tools

Online Tools/Calculators

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.

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

UWPR computing resources (as of 9/2022)

  • Two (2) Dell PowerEdge R6515 servers each with 256GB RAM, 480GB SSD, and dual AMD EPYC 7443P 2.85GHz CPUs (each with 24 cores, 48 threads, 128M Cache). These serve as compute servers.
  • One (1) Dell PowerEdge R520 server with 64GB RAM, Intel Xeon E5-2470 2.3GHz CPU (8 core, 16 threads, 20M Cache), PERC H710p RAID controller with 8 1TB SATA drives. This serves as an application and web server.
  • 23TB of enterprise class storage with NFS (Linux) and SMB (Windows) connectivity.
  • The UWPR also has access to UW Genome Sciences cluster computing resources. This includes (A) one compute node with dual Intel Xeon Gold 6330N 2.2GHz CPUs (each with 28 cores, 56 threads, 42MB cache), 512GB RAM, 890GB local storage; (B) two compute nodes with dual Intel Xeon Silver 4316 2.3GHz CPUs (each with 20 cores, 40 threads, 30MB cache), 256GB RAM, 890GB local storage; and (C) three compute nodes with Intel Xeon E5-2680 2.5GHz CPUs (8 cores, 16 threads, 20MB cache), 256GB RAM, 930GB local storage.