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Complete De Novo Assembly of Monoclonal Antibody Sequences

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Complete De Novo Assembly of Monoclonal Antibody Sequences

Ngoc Hieu Tran et al. Sci Rep.

Abstract

De novo protein sequencing is one of the key problems in mass spectrometry-based proteomics, especially for novel proteins such as monoclonal antibodies for which genome information is often limited or not available. However, due to limitations in peptides fragmentation and coverage, as well as ambiguities in spectra interpretation, complete de novo assembly of unknown protein sequences still remains challenging. To address this problem, we propose an integrated system, ALPS, which for the first time can automatically assemble full-length monoclonal antibody sequences. Our system integrates de novo sequencing peptides, their quality scores and error-correction information from databases into a weighted de Bruijn graph to assemble protein sequences. We evaluated ALPS performance on two antibody data sets, each including a heavy chain and a light chain. The results show that ALPS was able to assemble three complete monoclonal antibody sequences of length 216-441 AA, at 100% coverage, and 96.64-100% accuracy.

Figures

Figure 1
Figure 1. ALPS system for automated and complete de novo assembly of monoclonal antibody sequences.
Figure 2
Figure 2. Assembly results for the WIgG1 light chain.
(A) BLAST alignment of the top assembled contigs from list PSM-DN against the target light chain. (B) Zoom-in details of the alignment in (A). (C) BLAST alignment of the full-length contig assembled from list PSM-DD against the target light chain. (D) Details of the alignment in (C).
Figure 3
Figure 3. Assembly results for the WIgG1 heavy chain.
(A) BLAST alignment of the top assembled contigs from list PSM-DN against the target heavy chain. (B) BLAST alignment of the full-length contig assembled from list PSM-DDS against the target heavy chain. (C) Details of the alignment in (B).
Figure 4
Figure 4. Assembly results for the HUMAN heavy chain.
(A) BLAST alignment of the top assembled contigs from list PSM-DDS against the target heavy chain. (B) BLAST alignment of the template-alignment-based merging of PSM-DDS contigs against the target heavy chain. (C) Details of the alignment in (B).

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