Software for constructing, quantifying, and visualizing proteoform families.
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.
Video tutorial on how to use Proteoform Suite:
Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families (2017, Anal. Chem.)
- The release and vignette for top-down 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 version used for this analysis can be found here.
Vignettes are housed in releases and also at this repository.
- Proteoform Identification: Proteoform are identified from measurements of intact mass and 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 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.
The following files must be obtained and installed:
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uniprot.xml: A UniProt reference database in .xml format
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ptmlist.txt: A PTM library
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for thermo .RAW files: Thermo MSFileReader
- 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.
- 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.
The software is currently released under the GNU GPLv3.
Copyright 2016