Literature DB >> 31050378

Identification and Quantification of Proteoforms by Mass Spectrometry.

Leah V Schaffer1, Robert J Millikin1, Rachel M Miller1, Lissa C Anderson2, Ryan T Fellers3, Ying Ge1,4, Neil L Kelleher3,5, Richard D LeDuc3, Xiaowen Liu6,7, Samuel H Payne8, Liangliang Sun9, Paul M Thomas3, Trisha Tucholski1, Zhe Wang10, Si Wu10, Zhijie Wu1, Dahang Yu10, Michael R Shortreed1, Lloyd M Smith1.   

Abstract

A proteoform is a defined form of a protein derived from a given gene with a specific amino acid sequence and localized post-translational modifications. In top-down proteomic analyses, proteoforms are identified and quantified through mass spectrometric analysis of intact proteins. Recent technological developments have enabled comprehensive proteoform analyses in complex samples, and an increasing number of laboratories are adopting top-down proteomic workflows. In this review, some recent advances are outlined and current challenges and future directions for the field are discussed.
© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  bioinformatics; mass spectrometry; proteoform; proteoform family; top-down proteomics

Mesh：

Substances：

Year:  2019        PMID： 31050378      PMCID： PMC6602557          DOI： 10.1002/pmic.201800361

Source DB:  PubMed          Journal:  Proteomics        ISSN： 1615-9853            Impact factor:   3.984


  149 in total

1.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.

Authors:  Joshua E Elias; Steven P Gygi
Journal:  Nat Methods       Date:  2007-03       Impact factor: 28.547

2.  Chain length dependence of apomyoglobin folding: structural evolution from misfolded sheets to native helices.

Authors:  Clement C Chow; Charles Chow; Vinodhkumar Raghunathan; Theodore J Huppert; Erin B Kimball; Silvia Cavagnero
Journal:  Biochemistry       Date:  2003-06-17       Impact factor: 3.162

Review 3.  Top-down proteomics in health and disease: challenges and opportunities.

Authors:  Zachery R Gregorich; Ying Ge
Journal:  Proteomics       Date:  2014-05       Impact factor: 3.984

4.  New mass-spectrometry-compatible degradable surfactant for tissue proteomics.

Authors:  Ying-Hua Chang; Zachery R Gregorich; Albert J Chen; Leekyoung Hwang; Huseyin Guner; Deyang Yu; Jianyi Zhang; Ying Ge
Journal:  J Proteome Res       Date:  2015-01-30       Impact factor: 4.466

5.  Robust analysis of the yeast proteome under 50 kDa by molecular-mass-based fractionation and top-down mass spectrometry.

Authors:  John F Kellie; Adam D Catherman; Kenneth R Durbin; John C Tran; Jeremiah D Tipton; Jeremy L Norris; Charles E Witkowski; Paul M Thomas; Neil L Kelleher
Journal:  Anal Chem       Date:  2011-12-14       Impact factor: 6.986

6.  Ion mobility-mass spectrometry (IM-MS) for top-down proteomics: increased dynamic range affords increased sequence coverage.

Authors:  Nathanael F Zinnel; Pei-Jing Pai; David H Russell
Journal:  Anal Chem       Date:  2012-03-22       Impact factor: 6.986

Review 7.  Top-Down Proteomics: Ready for Prime Time?

Authors:  Bifan Chen; Kyle A Brown; Ziqing Lin; Ying Ge
Journal:  Anal Chem       Date:  2017-12-15       Impact factor: 6.986

8.  Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms Between Mouse Strains.

Authors:  Roderick G Davis; Hae-Min Park; Kyunggon Kim; Joseph B Greer; Ryan T Fellers; Richard D LeDuc; Elena V Romanova; Stanislav S Rubakhin; Jonathan A Zombeck; Cong Wu; Peter M Yau; Peng Gao; Alexandra J van Nispen; Steven M Patrie; Paul M Thomas; Jonathan V Sweedler; Justin S Rhodes; Neil L Kelleher
Journal:  Anal Chem       Date:  2018-02-26       Impact factor: 6.986

9.  MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.

Authors:  Andy T Kong; Felipe V Leprevost; Dmitry M Avtonomov; Dattatreya Mellacheruvu; Alexey I Nesvizhskii
Journal:  Nat Methods       Date:  2017-04-10       Impact factor: 28.547

10.  Protein charge distribution in proteomes and its impact on translation.

Authors:  Rodrigo D Requião; Luiza Fernandes; Henrique José Araujo de Souza; Silvana Rossetto; Tatiana Domitrovic; Fernando L Palhano
Journal:  PLoS Comput Biol       Date:  2017-05-22       Impact factor: 4.475
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  43 in total

1.  Sequencing a Bispecific Antibody by Controlling Chain Concentration Effects When Using an Immobilized Nonspecific Protease.

Authors:  Robert A D'Ippolito; Maria C Panepinto; Keira E Mahoney; Dina L Bai; Jeffrey Shabanowitz; Donald F Hunt
Journal:  Anal Chem       Date:  2020-07-13       Impact factor: 6.986

2.  PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping.

Authors:  Luis Francisco Hernández Sánchez; Bram Burger; Carlos Horro; Antonio Fabregat; Stefan Johansson; Pål Rasmus Njølstad; Harald Barsnes; Henning Hermjakob; Marc Vaudel
Journal:  Gigascience       Date:  2019-08-01       Impact factor: 6.524

Review 3.  High-throughput quantitative top-down proteomics.

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

Review 4.  Proteomics and Metabolomics in Kidney Disease, including Insights into Etiology, Treatment, and Prevention.

Authors:  Ruth F Dubin; Eugene P Rhee
Journal:  Clin J Am Soc Nephrol       Date:  2019-10-21       Impact factor: 8.237

5.  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

6.  Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data.

Authors:  Leah V Schaffer; Robert J Millikin; Michael R Shortreed; Mark Scalf; Lloyd M Smith
Journal:  J Proteome Res       Date:  2020-07-10       Impact factor: 4.466

7.  Predicting Electrophoretic Mobility of Proteoforms for Large-Scale Top-Down Proteomics.

Authors:  Daoyang Chen; Rachele A Lubeckyj; Zhichang Yang; Elijah N McCool; Xiaojing Shen; Qianjie Wang; Tian Xu; Liangliang Sun
Journal:  Anal Chem       Date:  2020-02-17       Impact factor: 6.986

8.  Increased Single-Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading.

Authors:  Chad R Weisbrod; Lissa C Anderson; Joseph B Greer; Caroline J DeHart; Christopher L Hendrickson
Journal:  Anal Chem       Date:  2020-09-02       Impact factor: 6.986

9.  MASH Explorer: A Universal Software Environment for Top-Down Proteomics.

Authors:  Zhijie Wu; David S Roberts; Jake A Melby; Kent Wenger; Molly Wetzel; Yiwen Gu; Sudharshanan Govindaraj Ramanathan; Elizabeth F Bayne; Xiaowen Liu; Ruixiang Sun; Irene M Ong; Sean J McIlwain; Ying Ge
Journal:  J Proteome Res       Date:  2020-08-24       Impact factor: 4.466

10.  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
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