Software for constructing, quantifying, and visualizing proteoform families.

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 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.

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

• 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.

• 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 Just Accepted

• 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

The software is currently released under the GNU GPLv3.

Copyright 2016