Literature DB >> 29195273

Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

Anthony J Cesnik1, Michael R Shortreed1, Leah V Schaffer1, Rachel A Knoener1, Brian L Frey1, Mark Scalf1, Stefan K Solntsev1, Yunxiang Dai1, Audrey P Gasch1, Lloyd M Smith1.   

Abstract

We present an open-source, interactive program named Proteoform Suite that uses proteoform mass and intensity measurements from complex biological samples to identify and quantify proteoforms. It constructs families of proteoforms derived from the same gene, assesses proteoform function using gene ontology (GO) analysis, and enables visualization of quantified proteoform families and their changes. It is applied here to reveal systemic proteoform variations in the yeast response to salt stress.

Entities:  

Keywords:  NeuCode; PTM; identification; intact mass; lysine count; modification; proteoform; quantification; visualization

Mesh：

Substances：

Year:  2017        PMID： 29195273      PMCID： PMC5770237          DOI： 10.1021/acs.jproteome.7b00685

Source DB:  PubMed          Journal:  J Proteome Res        ISSN： 1535-3893            Impact factor:   4.466


  31 in total

1.  Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions.

Authors:  M W Senko; S C Beu; F W McLaffertycor
Journal:  J Am Soc Mass Spectrom       Date:  1995-04       Impact factor: 3.109

Review 2.  Top Down proteomics: facts and perspectives.

Authors:  Adam D Catherman; Owen S Skinner; Neil L Kelleher
Journal:  Biochem Biophys Res Commun       Date:  2014-02-17       Impact factor: 3.575

3.  Continuous Elution Proteoform Identification of Myelin Basic Protein by Superficially Porous Reversed-Phase Liquid Chromatography and Fourier Transform Mass Spectrometry.

Authors:  Daniel A Plymire; Casey E Wing; Dana E Robinson; Steven M Patrie
Journal:  Anal Chem       Date:  2017-10-31       Impact factor: 6.986

4.  Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database.

Authors:  Yunxiang Dai; Michael R Shortreed; Mark Scalf; Brian L Frey; Anthony J Cesnik; Stefan Solntsev; Leah V Schaffer; Lloyd M Smith
Journal:  J Proteome Res       Date:  2017-11-03       Impact factor: 4.466

5.  Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation.

Authors:  Nicholas M Riley; Christopher Mullen; Chad R Weisbrod; Seema Sharma; Michael W Senko; Vlad Zabrouskov; Michael S Westphall; John E P Syka; Joshua J Coon
Journal:  J Am Soc Mass Spectrom       Date:  2015-11-20       Impact factor: 3.109

6.  Neutron-encoded mass signatures for multiplexed proteome quantification.

Authors:  Alexander S Hebert; Anna E Merrill; Derek J Bailey; Amelia J Still; Michael S Westphall; Eric R Strieter; David J Pagliarini; Joshua J Coon
Journal:  Nat Methods       Date:  2013-02-24       Impact factor: 28.547

7.  Cytoscape 2.8: new features for data integration and network visualization.

Authors:  Michael E Smoot; Keiichiro Ono; Johannes Ruscheinski; Peng-Liang Wang; Trey Ideker
Journal:  Bioinformatics       Date:  2010-12-12       Impact factor: 6.937

8.  Global Post-Translational Modification Discovery.

Authors:  Qiyao Li; Michael R Shortreed; Craig D Wenger; Brian L Frey; Leah V Schaffer; Mark Scalf; Lloyd M Smith
Journal:  J Proteome Res       Date:  2017-03-01       Impact factor: 4.466

9.  Neutron-encoded mass signatures for quantitative top-down proteomics.

Authors:  Timothy W Rhoads; Christopher M Rose; Derek J Bailey; Nicholas M Riley; Rosalynn C Molden; Amelia J Nestler; Anna E Merrill; Lloyd M Smith; Alexander S Hebert; Michael S Westphall; David J Pagliarini; Benjamin A Garcia; Joshua J Coon
Journal:  Anal Chem       Date:  2014-02-19       Impact factor: 6.986

10.  Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements.

Authors:  Michael R Shortreed; Brian L Frey; Mark Scalf; Rachel A Knoener; Anthony J Cesnik; Lloyd M Smith
Journal:  J Proteome Res       Date:  2016-03-16       Impact factor: 4.466
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  14 in total

Review 1.  High-throughput quantitative top-down proteomics.

Authors:  Kellye A Cupp-Sutton; Si Wu
Journal:  Mol Omics       Date:  2020-01-14

2.  Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families.

Authors:  Leah V Schaffer; Michael R Shortreed; Anthony J Cesnik; Brian L Frey; Stefan K Solntsev; Mark Scalf; Lloyd M Smith
Journal:  Anal Chem       Date:  2017-12-22       Impact factor: 6.986

3.  Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms.

Authors:  Leah V Schaffer; Trisha Tucholski; Michael R Shortreed; Ying Ge; Lloyd M Smith
Journal:  Anal Chem       Date:  2019-08-14       Impact factor: 6.986

Review 4.  Identification and Quantification of Proteoforms by Mass Spectrometry.

Authors:  Leah V Schaffer; Robert J Millikin; Rachel M Miller; Lissa C Anderson; Ryan T Fellers; Ying Ge; Neil L Kelleher; Richard D LeDuc; Xiaowen Liu; Samuel H Payne; Liangliang Sun; Paul M Thomas; Trisha Tucholski; Zhe Wang; Si Wu; Zhijie Wu; Dahang Yu; Michael R Shortreed; Lloyd M Smith
Journal:  Proteomics       Date:  2019-05       Impact factor: 3.984

5.  Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database.

Authors:  Yunxiang Dai; Katherine E Buxton; Leah V Schaffer; Rachel M Miller; Robert J Millikin; Mark Scalf; Brian L Frey; Michael R Shortreed; Lloyd M Smith
Journal:  J Proteome Res       Date:  2019-09-18       Impact factor: 4.466

6.  Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy.

Authors:  Leah V Schaffer; Jarred W Rensvold; Michael R Shortreed; Anthony J Cesnik; Adam Jochem; Mark Scalf; Brian L Frey; David J Pagliarini; Lloyd M Smith
Journal:  J Proteome Res       Date:  2018-09-18       Impact factor: 4.466

7.  Top-down proteomics: challenges, innovations, and applications in basic and clinical research.

Authors:  Kyle A Brown; Jake A Melby; David S Roberts; Ying Ge
Journal:  Expert Rev Proteomics       Date:  2020-12-17       Impact factor: 3.940

Review 8.  Novel Strategies to Address the Challenges in Top-Down Proteomics.

Authors:  Jake A Melby; David S Roberts; Eli J Larson; Kyle A Brown; Elizabeth F Bayne; Song Jin; Ying Ge
Journal:  J Am Soc Mass Spectrom       Date:  2021-05-13       Impact factor: 3.109

9.  Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis.

Authors:  Chad R Weisbrod; Lissa C Anderson; Christopher L Hendrickson; Leah V Schaffer; Michael R Shortreed; Lloyd M Smith; Jeffrey Shabanowitz; Donald F Hunt
Journal:  Anal Chem       Date:  2021-06-24       Impact factor: 8.008

10.  Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data.

Authors:  Leah V Schaffer; Lissa C Anderson; David S Butcher; Michael R Shortreed; Rachel M Miller; Caitlin Pavelec; Lloyd M Smith
Journal:  J Proteome Res       Date:  2020-10-19       Impact factor: 4.466
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