SPECTRUM - A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data.
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ArticleAuthors
Basharat, Abdul RehmanIman, Kanzal
Khalid, Muhammad Farhan
Anwar, Zohra
Hussain, Rashid
Kabir, Humnah Gohar
Tahreem, Maria
Shahid, Anam
Humayun, Maheen
Hayat, Hira Azmat
Mustafa, Muhammad
Shoaib, Muhammad Ali
Ullah, Zakir
Zarina, Shamshad
Ahmed, Sameer
Uddin, Emad
Hamera, Sadia
Ahmad, Fayyaz
Chaudhary, Safee Ullah

KAUST Department
Competitive Research FundsDate
2019-08-02Online Publication Date
2019-08-02Print Publication Date
2019-12Permanent link to this record
http://hdl.handle.net/10754/656468
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Show full item recordAbstract
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 against salient TDP tools. SPECTRUM provides significantly enhanced protein identification rates (91% to 177%) over its contemporaries. SPECTRUM has been implemented in MATLAB, and is freely available along with its source code and documentation at https://github.com/BIRL/SPECTRUM/.Citation
Basharat, A. R., Iman, K., Khalid, M. F., Anwar, Z., Hussain, R., Kabir, H. G., … Chaudhary, S. U. (2019). SPECTRUM – A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data. Scientific Reports, 9(1). doi:10.1038/s41598-019-47724-1Sponsors
We acknowledge the support provided by Osama Shiraz Shah for the fruitful discussions and suggestions during the development of the toolbox. This work was supported by HEC (21-320SRGP/R&D/HEC/2014, 20-2269/NRPU/R&D/ HEC/12/4792 and 20-3629/NRPU/R&D/HEC/14/585), Ignite (SRG-209), TWAS (RG 14-319 RG/ITC/AS_C) and LUMS (STG-BIO-1008, FIF-BIO-2052 and FIF-BIO-0255) grants.Publisher
Springer Science and Business Media LLCJournal
Scientific reportsAdditional Links
http://www.nature.com/articles/s41598-019-47724-1ae974a485f413a2113503eed53cd6c53
10.1038/s41598-019-47724-1
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