Literature DB >> 35657589

Top-Down Mass Spectrometry Data Analysis Using TopPIC Suite.

In Kwon Choi1, Xiaowen Liu2.   

Abstract

With the advances of mass spectrometry (MS) techniques, top-down MS-based proteomics has gained increasing attention because of its advantages over bottom-up MS in studying complex proteoforms. TopPIC Suite is a widely used software package for top-down MS-based proteoform identification and quantification. Here, we present the methods for top-down MS data analysis using TopPIC Suite.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Proteoform identification; Proteoform quantification; Proteomics; Spectral deconvolution; Top-down mass spectrometry

Mesh：

Substances：

Year:  2022        PMID： 35657589     DOI： 10.1007/978-1-0716-2325-1_8

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  10 in total

1.  Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach.

Authors:  Xiaowen Liu; Yuval Inbar; Pieter C Dorrestein; Colin Wynne; Nathan Edwards; Puneet Souda; Julian P Whitelegge; Vineet Bafna; Pavel A Pevzner
Journal:  Mol Cell Proteomics       Date:  2010-09-20       Impact factor: 5.911

2.  EnvCNN: A Convolutional Neural Network Model for Evaluating Isotopic Envelopes in Top-Down Mass-Spectral Deconvolution.

Authors:  Abdul Rehman Basharat; Xia Ning; Xiaowen Liu
Journal:  Anal Chem       Date:  2020-05-13       Impact factor: 6.986

3.  Identification of ultramodified proteins using top-down tandem mass spectra.

Authors:  Xiaowen Liu; Shawna Hengel; Si Wu; Nikola Tolić; Ljiljana Pasa-Tolić; Pavel A Pevzner
Journal:  J Proteome Res       Date:  2013-11-15       Impact factor: 4.466

4.  A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.

Authors:  Qiang Kou; Si Wu; Nikola Tolic; Ljiljana Paša-Tolic; Yunlong Liu; Xiaowen Liu
Journal:  Bioinformatics       Date:  2017-05-01       Impact factor: 6.937

5.  Proteomics in translational cancer research: biomarker discovery for clinical applications.

Authors:  William C S Cho
Journal:  Expert Rev Proteomics       Date:  2014-04       Impact factor: 3.940

Review 6.  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

7.  TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization.

Authors:  Qiang Kou; Likun Xun; Xiaowen Liu
Journal:  Bioinformatics       Date:  2016-07-16       Impact factor: 6.937

Review 8.  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

Review 9.  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

10.  ProteoWizard: open source software for rapid proteomics tools development.

Authors:  Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick
Journal:  Bioinformatics       Date:  2008-07-07       Impact factor: 6.937
  10 in total

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