Kira Vyatkina

Lennard J. M. Dekker

Ljiljana Paša-Tolić

Martijn M. VanDuijn

Nikola Tolić

Pavel A. Pevzner

Si Wu

Theo M. Luider

Xiaowen Liu

English

Abstract
               Motivation: Recent technological advances have made high-resolution mass spectrometers affordable to many laboratories, thus boosting rapid development of top-down mass spectrometry, and implying a need in efficient methods for analyzing this kind of data.
               Results: We describe a method for analysis of protein samples from top-down tandem mass spectrometry data, which capitalizes on de novo sequencing of fragments of the proteins present in the sample. Our algorithm takes as input a set of de novo amino acid strings derived from the given mass spectra using the recently proposed Twister approach, and combines them into aggregated strings endowed with offsets. The former typically constitute accurate sequence fragments of sufficiently well-represented proteins from the sample being analyzed, while the latter indicate their location in the protein sequence, and also bear information on post-translational modifications and fragmentation patterns.
               Availability and Implementation: Freely available on the web at http://bioinf.spbau.ru/en/twister.
               Contact:  vyatkina@spbau.ru or ppevzner@ucsd.edu
               Supplementary information:  Supplementary data are available at Bioinformatics online.</jats:p

Crossref

Bioinformatics

Top-down analysis of protein samples by <i>de novo</i> sequencing techniques

https://scholarworks.iupui.edu/bitstream/1805/13133/1/Vyatkina_2016_top-down.pdf

Top-down analysis of protein samples by
                    de novo

Top-down analysis of protein samples by de novo

Abstract

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