Literature DB >> 35657592

Mass Deconvolution of Top-Down Mass Spectrometry Datasets by FLASHDeconv.

Kyowon Jeong1, Jihyung Kim2, Oliver Kohlbacher2.   

Abstract

Mass deconvolution, the determination of proteoform precursor and fragment masses, is crucial for top-down proteomics data analysis. Here we describe the detailed procedure to run FLASHDeconv, an ultrafast, high-quality mass deconvolution tool. Both spectrum- and feature-level deconvolution results are obtainable in various output formats by FLASHDeconv. FLASHDeconv is runnable in different environments such as the command line and OpenMS workflows.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Feature deconvolution; Intact protein analysis; Mass deconvolution; Protein characterization; Top-down proteomics

Mesh：

Year:  2022        PMID： 35657592     DOI： 10.1007/978-1-0716-2325-1_11

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


  13 in total

1.  MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.

Authors:  Wenxuan Cai; Huseyin Guner; Zachery R Gregorich; Albert J Chen; Serife Ayaz-Guner; Ying Peng; Santosh G Valeja; Xiaowen Liu; Ying Ge
Journal:  Mol Cell Proteomics       Date:  2015-11-23       Impact factor: 5.911

2.  New and automated MSn approaches for top-down identification of modified proteins.

Authors:  Vlad Zabrouskov; Michael W Senko; Yi Du; Richard D Leduc; Neil L Kelleher
Journal:  J Am Soc Mass Spectrom       Date:  2005-10-25       Impact factor: 3.109

3.  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

4.  OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

Authors:  Hannes L Röst; Timo Sachsenberg; Stephan Aiche; Chris Bielow; Hendrik Weisser; Fabian Aicheler; Sandro Andreotti; Hans-Christian Ehrlich; Petra Gutenbrunner; Erhan Kenar; Xiao Liang; Sven Nahnsen; Lars Nilse; Julianus Pfeuffer; George Rosenberger; Marc Rurik; Uwe Schmitt; Johannes Veit; Mathias Walzer; David Wojnar; Witold E Wolski; Oliver Schilling; Jyoti S Choudhary; Lars Malmström; Ruedi Aebersold; Knut Reinert; Oliver Kohlbacher
Journal:  Nat Methods       Date:  2016-08-30       Impact factor: 28.547

5.  FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics.

Authors:  Kyowon Jeong; Jihyung Kim; Manasi Gaikwad; Siti Nurul Hidayah; Laura Heikaus; Hartmut Schlüter; Oliver Kohlbacher
Journal:  Cell Syst       Date:  2020-02-19       Impact factor: 10.304

Review 6.  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 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.  An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes.

Authors:  Huilin Li; Hong Hanh Nguyen; Rachel R Ogorzalek Loo; Iain D G Campuzano; Joseph A Loo
Journal:  Nat Chem       Date:  2018-01-01       Impact factor: 24.427

9.  Informed-Proteomics: open-source software package for top-down proteomics.

Authors:  Jungkap Park; Paul D Piehowski; Christopher Wilkins; Mowei Zhou; Joshua Mendoza; Grant M Fujimoto; Bryson C Gibbons; Jared B Shaw; Yufeng Shen; Anil K Shukla; Ronald J Moore; Tao Liu; Vladislav A Petyuk; Nikola Tolić; Ljiljana Paša-Tolić; Richard D Smith; Samuel H Payne; Sangtae Kim
Journal:  Nat Methods       Date:  2017-08-07       Impact factor: 28.547

Review 10.  Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.

Authors:  Daniel P Donnelly; Catherine M Rawlins; Caroline J DeHart; Luca Fornelli; Luis F Schachner; Ziqing Lin; Jennifer L Lippens; Krishna C Aluri; Richa Sarin; Bifan Chen; Carter Lantz; Wonhyeuk Jung; Kendall R Johnson; Antonius Koller; Jeremy J Wolff; Iain D G Campuzano; Jared R Auclair; Alexander R Ivanov; Julian P Whitelegge; Ljiljana Paša-Tolić; Julia Chamot-Rooke; Paul O Danis; Lloyd M Smith; Yury O Tsybin; Joseph A Loo; Ying Ge; Neil L Kelleher; Jeffrey N Agar
Journal:  Nat Methods       Date:  2019-06-27       Impact factor: 28.547
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.