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

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

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...

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Bibliographic Details
Main Author: Kira Vyatkina
Format: Article
Language:English
Published: MDPI AG 2017-02-01
Series:Proteomes
Subjects:
top-down mass spectrometry
de novo sequencing
tag convolution
Online Access:http://www.mdpi.com/2227-7382/5/1/6
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spelling doaj-ef628cc03d0d47f0ac40ff6122f5f35f2020-11-24T21:21:48ZengMDPI AGProteomes2227-73822017-02-0151610.3390/proteomes5010006proteomes5010006De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein SequenceKira Vyatkina0Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, 7-9 Universitetskaya nab., St. Petersburg 199034, RussiaDe 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.http://www.mdpi.com/2227-7382/5/1/6top-down mass spectrometryde novo sequencingtag convolution
collection DOAJ
language English
format Article
sources DOAJ
author Kira Vyatkina
spellingShingle Kira Vyatkina
De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence
Proteomes
top-down mass spectrometry
de novo sequencing
tag convolution
author_facet Kira Vyatkina
author_sort Kira Vyatkina
title De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence
title_short De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence
title_full De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence
title_fullStr De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence
title_full_unstemmed De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence
title_sort de novo sequencing of top-down tandem mass spectra: a next step towards retrieving a complete protein sequence
publisher MDPI AG
series Proteomes
issn 2227-7382
publishDate 2017-02-01
description 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.
topic top-down mass spectrometry
de novo sequencing
tag convolution
url http://www.mdpi.com/2227-7382/5/1/6
work_keys_str_mv AT kiravyatkina denovosequencingoftopdowntandemmassspectraanextsteptowardsretrievingacompleteproteinsequence
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