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README.md

Proteoform Suite

Software for constructing, quantifying, and visualizing proteoform families. Build status codecov Codacy Badge

Papers and Software Releases

The most current release can be found here.

Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. (2017, J. Proteome Res.)

  • The release and vignette for this analysis can be found here.

Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families (2017, Anal. Chem.)

  • The release and vignette for this analysis can be found here.

Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. (2017, J. Proteome Res.)

  • The release for this analysis can be found here.

Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy. (2018, J. Proteome Res.)

  • The release and vignette for this analysis can be found here.

Vignettes are housed in releases and also at this repository.

Video tutorial on how to use Proteoform Suite: Proteoform Suite Tutorial

Functionality

  • Proteoform Identification: Proteoform are identified from measurements of intact mass and optionally lysine count.
  • Custom Database: PTMs archived and UniProt and discovered using G-PTM-D or MetaMopheus are used in the construction of theoretical proteoforms.
  • Quantification: NeuCode-labeled or unlabeled proteoform intensity ratios are calculated from separate analysis files following proteoform identification.
  • Gene Ontology Analysis: Performed alongside quantification based on proteoforms that are significantly induced or repressed. GO terms are obtained from UniProt protein annotations.
  • Visualization: ProteoformSuite facilitates the visualization of the relationships between proteoforms by creating scripts to load in the network visualization program Cytoscape.

Requirements

The following files must be obtained and installed:

System Requirements and Usage for Release Version

  • 8 GB of RAM is recommended for yeast; more RAM is required for larger databases.
  • For visualization of proteoform families: Need to have Cytoscape 3.5.0.
  • For visualization of quantitative proteoform families: Need to install enhancedGraphics in Cytoscape using the App Manager under the Tools menu.
  • For thermo .RAW files: Need to have Thermo MSFileReader 3.1 SP2 installed.

System Requirements for Editing Solution

  • Visual Studio 2017 Version 15.1
  • Microsoft .NET Framework Version 4.6
  • 16 GB of RAM is recommended
  • For visualization of quantitative proteoform families: Need to install enhancedGraphics in Cytoscape using the App Manager under the Tools menu.
  • For thermo .RAW files: Need to have Thermo MSFileReader 3.1 SP2 installed.

References

License

The software is currently released under the GNU GPLv3.

Copyright 2016

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