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West Ashley Library
9 a.m. - 5 p.m.
Phone: (843) 766-6635
Wando Mount Pleasant Library
9 a.m. - 5 p.m.
Phone: (843) 805-6888
Village Library
9 a.m. - 1 p.m.
Phone: (843) 884-9741
St. Paul's/Hollywood Library
9 a.m. - 5 p.m.
Phone: (843) 889-3300
Otranto Road Library
9 a.m. - 5 p.m.
Phone: (843) 572-4094
Mt. Pleasant Library
9 a.m. – 5 p.m.
Phone: (843) 849-6161
McClellanville Library
9 a.m. – 1 p.m.
Phone: (843) 887-3699
Keith Summey North Charleston Library
9 a.m. - 5 p.m.
Phone: (843) 744-2489
John's Island Library
9 a.m. - 5 p.m.
Phone: (843) 559-1945
Hurd/St. Andrews Library
9 a.m. - 5 p.m.
Phone: (843) 766-2546
Folly Beach Library
9 a.m. - 2 p.m.
*open the 2nd and 4th Saturday
*open the 2nd and 4th Saturday
Phone: (843) 588-2001
Edisto Island Library
9 a.m. - 1 p.m.
Phone: (843) 869-2355
Dorchester Road Library
9 a.m. - 5 p.m.
Phone: (843) 552-6466
John L. Dart Library
9 a.m. - 5 p.m.
Phone: (843) 722-7550
Baxter-Patrick James Island
9 a.m. - 5 p.m.
Phone: (843) 795-6679
Main Library
9 a.m. - 5 p.m.
Phone: (843) 805-6930
Bees Ferry West Ashley Library
9 a.m. - 5 p.m.
Phone: (843) 805-6892
Edgar Allan Poe/Sullivan's Island Library
Closed for renovations
Phone: (843) 883-3914
Mobile Library
Closed
Phone: (843) 805-6909
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Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly.
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- Author(s): Beslic, Denis1 (AUTHOR) ; Tscheuschner, Georg2 (AUTHOR) ; Renard, Bernhard Y3 (AUTHOR) ; Weller, Michael G2 (AUTHOR) ; Muth, Thilo2 (AUTHOR)
- Source:
Briefings in Bioinformatics. Jan2023, Vol. 24 Issue 1, p1-12. 12p.- Subject Terms:
- Source:
- Additional Information
- Subject Terms:
- Abstract: Monoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody–antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a valuable method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. In this study, we evaluated six recently developed de novo peptide sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, PointNovo and Casanovo), which were not specifically designed for antibody data. We validated their ability to identify and assemble antibody sequences on three multi-enzymatic data sets. The deep learning-based tools Casanovo and PointNovo showed an increased peptide recall across different enzymes and data sets compared with spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra and peptides of various lengths. We achieved a sequence coverage of 97.69–99.53% on the light chains of three different antibody data sets using the de Bruijn assembler ALPS and the predictions from Casanovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies and hybrid approaches such as homology search to achieve high accuracy on long protein sequences. [ABSTRACT FROM AUTHOR]
- Abstract: Copyright of Briefings in Bioinformatics is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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