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.

De novo peptide sequencing by deep learning

“…In this section, we present a key downstream application of DeepNovo for complete de novo sequencing of mAbs. We trained the DeepNovo model with an in-house antibody database and used it to perform de novo peptide sequencing on two antibody datasets, the WIgG1 light and heavy chains of mouse (21). Note that the two testing datasets were not included in the training database.…”

“…This field has been actively studied over the past 20 y, and many de novo sequencing tools have been proposed, such as PepNovo, PEAKS, NovoHMM, MSNovo, pNovo, UniNovo, and Novor among others (6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). The recent "gold rush" into mAbs has undoubtedly elevated the application of de novo sequencing to a new horizon (20)(21)(22)(23). However, computational challenges still remain, because MS/MS spectra contain much noise and ambiguity that require rigorous global optimization with various forms of dynamic programming that have been developed over the past decade (8-10, 12, 13, 15-19, 24).…”

Hortense: Horizontal gene transfer detection directly from proteomic MS/MS data

“…If the donor proteome is not available at all, one could still opt for a de novo peptide sequencing approach to assemble the presumed HGT protein from the spectra that could not be mapped to the acceptor proteome (Muth & Renard, 2017). However, although de novo sequencing has been successfully applied for assembling full-length antibody sequences (Tran et al, 2016), the technique is still not as reliable as database searching and requires MS/MS spectra of high resolution and -even better-of different fragmentation modes to achieve a sufficient performance (Guthals et al, 2013).…”

De novo sequencing of proteins and peptides: algorithms, applications, perspectives

“…Необходимость в этом возникает, в частности, при разработке лекарственных препаратов на основе моноклональных антител, которые, согласно оценке экспертов, в последние годы занимают наибольшую долю фармацевтического рынка среди биопрепаратов (см., например, [73]). Поэтому неудивительно, что многие алгоритмы были либо целенаправленно разработаны для решения этой задачи [63,64,74], либо протестированы на наборах масс-спектрометрических данных для антител [30][31][32]68], а компания Bioinformatics Solutions -разработчик системы PEAKS -летом 2017 г. выпустила на рынок программный пакет PEAKS AB [74], предназначенный для de novo секвенирования антител и анализа их аминокислотных последовательностей. Все эти алгоритмы предназначены для анализа либо отдельных моноклональных антител, либо простых их смесей, называемых "коктейлями" (antibody coctails), однако недавно была предпринята попытка разработать алгоритм, позволяющий анализировать поликлональные антитела [75].…”