smith-chem-wisc/ProteoformSuite

Construction, quantification, and visualization of proteoform families

Proteoform Suite

Software for constructing, quantifying, and visualizing proteoform families.

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.

Proteoform Suite Manual (PDF)

Video tutorial on how to use Proteoform Suite

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:

• uniprot.xml: A UniProt reference database in .xml format

  http://www.uniprot.org

• ptmlist.txt: A PTM library

  http://www.uniprot.org/docs/ptmlist.txt

• for thermo .RAW files: Thermo MSFileReader

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

• Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements: J Proteome Res, 2016, 15 (4), pp 1213–1221.

• Global Post-translational Modification Discovery: J Proteome Res, 2016, 16 (4), pp 1383–1390.

• Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search: J Proteome Res, 2015, 14 (11), pp 4714–4720.

• A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra: J Proteome Res, 2013, 12 (3), pp 1377–1386.

License

The software is currently released under the GNU GPLv3.

Copyright 2016