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Complete De Novo Assembly of Monoclonal Antibody Sequences.

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.

SUBMITTER: Tran NH

PROVIDER: S-EPMC4999880 | biostudies-other | 2016

REPOSITORIES: biostudies-other

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Complete De Novo Assembly of Monoclonal Antibody Sequences.

Tran Ngoc Hieu NH Rahman M Ziaur MZ He Lin L Xin Lei L Shan Baozhen B Li Ming M

Scientific reports 20160826

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 ...[more]

PMID: 27562653

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