Ranked solutions to a class of combinatorial optimizations—with applications in mass spectrometry based peptide sequencing and a variant of directed paths in random media

2005 ◽  
Vol 354 ◽  
pp. 558-570 ◽  
Author(s):  
Timothy P. Doerr ◽  
Gelio Alves ◽  
Yi-Kuo Yu
Keyword(s):  
Mass Spectrometry ◽  
Random Media ◽  
Peptide Sequencing ◽  
Directed Paths

Algorithm Development of de novo Peptide Sequencing Via Tandem Mass Spectrometry

2011 ◽  
Vol 37 (12) ◽  
pp. 1278-1288 ◽  
Author(s):  
Han-Chang SUN ◽  
Ji-Yang ZHANG ◽  
Hui LIU ◽  
Wei ZHANG ◽  
Chang-Ming XU ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
De Novo ◽  
Peptide Sequencing ◽  
Tandem Mass ◽  
Algorithm Development

Direct sequencing of a disulfide-linked peptide with electrospray ionization tandem mass spectrometry

The Analyst ◽  
2015 ◽  
Vol 140 (8) ◽  
pp. 2623-2627 ◽  
Author(s):  
Gongyu Li ◽  
Jiying Pei ◽  
Yue Yin ◽  
Guangming Huang
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Corona Discharge ◽  
Electrospray Ionization ◽  
Disulfide Bonds ◽  
Direct Sequencing ◽  
Peptide Sequencing ◽  
Tandem Mass ◽  
Esi Ms ◽  
Ionization Tandem Mass Spectrometry

Enhanced corona discharge was employed for in-spray dissociation of disulfide bonds, facilitating disulfide-containing peptide sequencing with ESI-MS/MS.

ON PREPROCESSING AND ANTISYMMETRY IN DE NOVO PEPTIDE SEQUENCING: IMPROVING EFFICIENCY AND ACCURACY

2008 ◽  
Vol 06 (03) ◽  
pp. 467-492 ◽  
Author(s):  
KANG NING ◽  
NAN YE ◽  
HON WAI LEONG
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Computational Models ◽  
De Novo ◽  
Noise Removal ◽  
Peptide Sequencing ◽  
De Novo Sequencing ◽  
Tandem Mass ◽  
De Novo Peptide Sequencing ◽  
De Novo Peptide

Peptide sequencing plays a fundamental role in proteomics. Tandem mass spectrometry, being sensitive and efficient, is one of the most commonly used techniques in peptide sequencing. Many computational models and algorithms have been developed for peptide sequencing using tandem mass spectrometry. In this paper, we investigate general issues in de novo sequencing, and present results that can be used to improve current de novo sequencing algorithms. We propose a general preprocessing scheme that performs binning, pseudo-peak introduction, and noise removal, and present theoretical and experimental analyses on each of the components. Then, we study the antisymmetry problem and current assumptions related to it, and propose a more realistic way to handle the antisymmetry problem based on analysis of some datasets. We integrate our findings on preprocessing and the antisymmetry problem with some current models for peptide sequencing. Experimental results show that our findings help to improve accuracies for de novo sequencing.

scholarly journals De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry

2007 ◽  
Vol 6 (1) ◽  
pp. 114-123 ◽  
Author(s):  
Ari M. Frank ◽  
Mikhail M. Savitski ◽  
Michael L. Nielsen ◽  
Roman A. Zubarev ◽  
Pavel A. Pevzner
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
Peptide Sequencing ◽  
De Novo Peptide Sequencing ◽  
De Novo Peptide

Sign phase transition and directed paths in random media

JETP Letters ◽  
1996 ◽  
Vol 64 (4) ◽  
pp. 312-318 ◽  
Author(s):  
B. Spivak ◽  
S. Feng ◽  
F. Zeng
Keyword(s):  
Phase Transition ◽  
Random Media ◽  
Directed Paths
Sign in / Sign up

Export Citation Format

Share Document