Complete De Novo Assembly of Monoclonal Antibody Sequences

peer-reviewed · Scientific Reports · 2016

peer-reviewed · Scientific Reports · 2016. Ngoc Hieu Tran et al. De novo protein sequencing is one of the key problems in mass spectrometry-based proteomics, especially for…

Date	2016-08-26
Type	peer-reviewed
Venue	Scientific Reports
Publisher	Springer Science and Business Media LLC
Contribution	post-processor
DOI	10.1038/srep31730
Citations (OpenAlex)	165
Venue 2-year citedness	5.08

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.

Methods and tools

ALPS: Assembles de novo sequenced peptides and their per-residue confidence scores into a de Bruijn graph to reconstruct complete monoclonal antibody heavy and light chains without a template.

Data deposited

Monoclonal antibody de novo assembly (as deposited) · MSV000079801

Cites (16)

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Cited by (66)

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