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This is the home page for the CCMS Tools space. Documentation is available for the following CCMS tools:

  • Spectral Networks
  • SpecPlot - a tool for annotation of tandem mass spectra (MS/MS spectra, PRM spectra, etc)
  • Shotgun Protein Sequencing - usage information for protein sequencing using SPS (tailored to monoclonal antibody sequencing)
  • MS-GF - usage information for MS-GF - a tool that generates rigorous p-values of peptide-spectrum matches.
  • MS-Align+ - finds protein-spectrum matches.
  • Multiplex Denovo Sequencing - simultaneous Denovo sequencing of spectral networks of peptidic natural products.
  • [Multistage Denovo Sequencing] - sequencing non-linear peptides using multistage mass spectra.
  • Cycloquest - database search for non-linear ribosomal peptides.
  • [MSDPR] - computing statistical significance of peptide spectrum matches
  • [NRPquest] - discovering novel non-ribosomal peptides by mass spectrometry and genome mining.
  • [RiPPquest] - discovering novel ribosomally produced and post-translationally modified peptides by mass spectrometry and genome mining.

Missing documentation: 

  • InsPecT
  • PepNovo
  • MS-Cluster
  • MS-GF
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