SPECTRUM - A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data

Scientific Reports
Abdul Rehman BasharatSafee Ullah Chaudhary

Abstract

Top-Down Proteomics (TDP) is an emerging proteomics protocol that involves identification, characterization, and quantitation of intact proteins using high-resolution mass spectrometry. TDP has an edge over other proteomics protocols in that it allows for: (i) accurate measurement of intact protein mass, (ii) high sequence coverage, and (iii) enhanced identification of post-translational modifications (PTMs). However, the complexity of TDP spectra poses a significant impediment to protein search and PTM characterization. Furthermore, limited software support is currently available in the form of search algorithms and pipelines. To address this need, we propose 'SPECTRUM', an open-architecture and open-source toolbox for TDP data analysis. Its salient features include: (i) MS2-based intact protein mass tuning, (ii) de novo peptide sequence tag analysis, (iii) propensity-driven PTM characterization, (iv) blind PTM search, (v) spectral comparison, (vi) identification of truncated proteins, (vii) multifactorial coefficient-weighted scoring, and (viii) intuitive graphical user interfaces to access the aforementioned functionalities and visualization of results. We have validated SPECTRUM using published datasets and benchmarked it a...Continue Reading

References

Jul 1, 1995·Electrophoresis·V C WasingerI Humphery-Smith
Jun 26, 2003·Nucleic Acids Research·Elisabeth GasteigerAmos Bairoch
Nov 6, 2004·Nature Biotechnology·Patrick G A PedrioliRuedi Aebersold
Jul 15, 2005·Analytical Chemistry·Stephen TannerVineet Bafna
Nov 26, 2005·Expert Review of Proteomics·Simon M LinWarren A Kibbe
Jun 26, 2007·Nucleic Acids Research·Leonid ZamdborgNeil L Kelleher
Sep 29, 2007·Nature Methods·Nertila Siuti, Neil L Kelleher
Feb 28, 2008·Analytical Chemistry·Ari M FrankPavel A Pevzner
May 14, 2008·BioTechniques·Ming Zhou, Timothy Veenstra
Aug 23, 2008·Current Opinion in Chemical Biology·Xuemei HanJohn R Yates
Aug 29, 2009·Journal of Proteome Research·Pedro Navarro, Jesús Vázquez
Mar 12, 2010·Methods in Molecular Biology·Birgit Eisenhaber, Frank Eisenhaber
Sep 22, 2010·Molecular & Cellular Proteomics : MCP·Xiaowen LiuPavel A Pevzner
Sep 23, 2010·Proteomics·Andrea Armirotti, Gianluca Damonte
Nov 11, 2010·Methods in Molecular Biology·Michael Turewicz, Eric W Deutsch
Apr 12, 2011·Journal of Proteomics·David CalligarisDaniel Lafitte
May 7, 2011·Journal of Proteome Research·Lydia Ashleigh BaumgardnerDaniel B Martin
Sep 8, 2012·Molecular & Cellular Proteomics : MCP·Eric W Deutsch
Oct 12, 2012·Nature Biotechnology·Matthew C ChambersParag Mallick
Dec 22, 2012·Journal of Proteome Research·Ying PengYing Ge
Jan 2, 2013·Journal of Proteomics·Florent GluckAlexander Scherl
Jan 11, 2013·Chemical Reviews·María Eugenia MongeFacundo M Fernández
Feb 27, 2013·Chemical Reviews·Yaoyang ZhangJohn R Yates
Feb 28, 2013·Nature Methods·Lloyd M SmithUNKNOWN Consortium for Top Down Proteomics
May 28, 2013·Analytical Chemistry·John R Yates, Neil L Kelleher
Jun 29, 2013·Genome Medicine·John P SavarynNeil L Kelleher
Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates
Feb 26, 2014·BMC Genomics·Xiaowen LiuSangtae Kim
Apr 12, 2014·Proteomics·Zachery R Gregorich, Ying Ge
Nov 1, 2015·Methods in Molecular Biology·Suruchi Aggarwal, Amit Kumar Yadav
Jul 28, 2016·Expert Review of Proteomics·Wenxuan CaiYing Ge
Aug 31, 2016·Nature Methods·Hannes L RöstOliver Kohlbacher
Feb 12, 2017·Journal of Proteomics·Luca FornelliNeil L Kelleher
Aug 8, 2017·Nature Methods·Jungkap ParkSangtae Kim

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Citations

Mar 3, 2020·Briefings in Bioinformatics·Jiancheng ZhongJianxin Wang
Apr 16, 2021·Frontiers in Genetics·Eugenio Del PretePaolo Romano
May 18, 2021·Nucleic Acids Research·Muhammad Farhan KhalidSafee Ullah Chaudhary
Nov 14, 2020·Journal of Proteome Research·Wenrong Chen, Xiaowen Liu

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Methods Mentioned

BETA
electron-capture dissociation

Software Mentioned

Convert
MS
TDP
pTop
SEQUEST
MSPathFinder
TopPIC
Deconv
- Deconv
ExPASy

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