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This is the home page for the CCMS Tools space. Documentation is available for the following CCMS tools:
* Spectral Networks
** [Installation guide|CCMStools:Spectral Networks - Installation guide]  
** [Users guide|CCMStools:Spectral Networks - Users guide]
* [SpecPlot|CCMStools:SPECPLOT] \- a tool for annotation of tandem mass spectra (MS/MS spectra, PRM spectra, etc)
* [Shotgun Protein Sequencing|Shotgun Protein Sequencing - usage] \- usage information for protein sequencing using SPS (tailored to monoclonal antibody sequencing)
* [MS-GF|MS-GF] \- usage information for MS-GF - a tool that generates rigorous p-values of peptide-spectrum matches.
* [MS-Align\+|MS-Align+] \- finds protein-spectrum matches.
* [Multiplex Denovo Sequencing|Multiplex Denovo Sequencing] \- simultaneous Denovo sequencing of spectral networks of peptidic natural products.
* [Multistage Denovo Sequencing|Multstage Denovo Sequencing] \- sequencing non-linear peptides using multistage mass spectra.
* [Cycloquest|Cycloquest] \- database search for non-linear ribosomal peptides.
* [MSDPR|MSDPR] \- computing statistical significance of peptide spectrum matches
* [NRPquest|NRPquest] \- discovering novel non-ribosomal peptides by mass spectrometry and genome mining.
* [RiPPquest|RiPPquest] \- discovering novel ribosomally produced and post-translationally modified peptides by mass spectrometry and genome mining.


Missing documentation: 
* InsPecT
* PepNovo
* MS-Cluster
* MS-GF