De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence

peer-reviewed · Proteomes · 2017

peer-reviewed · Proteomes · 2017. Kira Vyatkina. De novo sequencing of tandem (MS/MS) mass spectra represents the only way to determine the sequence of…

Date	2017-02-08
Type	peer-reviewed
Venue	Proteomes
Publisher	MDPI AG
Contribution	algorithm
DOI	10.3390/proteomes5010006
Citations (OpenAlex)	26

Abstract

De novo sequencing of tandem (MS/MS) mass spectra represents the only way to determine the sequence of proteins from organisms with unknown genomes, or the ones not directly inscribed in a genome-such as antibodies, or novel splice variants. Top-down mass spectrometry provides new opportunities for analyzing such proteins; however, retrieving a complete protein sequence from top-down MS/MS spectra still remains a distant goal. In this paper, we review the state-of-the-art on this subject, and enhance our previously developed Twister algorithm for de novo sequencing of peptides from top-down MS/MS spectra to derive longer sequence fragments of a target protein.

Authors

Kira Vyatkina · ITMO University, Saint Petersburg Academic University, Saint Petersburg National Research Academic University of the Russian Academy of Sciences, Saint Petersburg State Electrotechnical University, St Petersburg University, St. Petersburg State University

Methods and tools

Top-down tandem spectrum de novo sequencing: De novo sequencing of top-down tandem mass spectra, aimed at the proteins no database can serve – organisms with unknown genomes, antibodies, novel splice variants – and at recovering a complete sequence rather than peptide-length fragments.

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Cited by (7)

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