Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo-peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms

2013 ◽  
Vol 28 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Ivan Terterov ◽  
Kira Vyatkina ◽  
Alexey S. Kononikhin ◽  
Vitali Boitsov ◽  
Sergey Vyazmin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Glutamic Acid ◽  
De Novo ◽  
De Novo Sequencing ◽  
Tandem Mass

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 A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Chongle Pan ◽  
Byung H Park ◽  
William H McDonald ◽  
Patricia A Carey ◽  
Jillian F Banfield ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Tandem Mass Spectrometry ◽  
High Throughput ◽  
De Novo ◽  
Shotgun Proteomics ◽  
De Novo Sequencing ◽  
Tandem Mass

scholarly journals De novo sequencing of peptides on single resin beads by MALDI-FTICR tandem mass spectrometry

2010 ◽  
Vol 21 (2) ◽  
pp. 215-219 ◽  
Author(s):  
Angelika Semmler ◽  
Reinhold Weber ◽  
Michael Przybylski ◽  
Valentin Wittmann
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
De Novo ◽  
De Novo Sequencing ◽  
Tandem Mass ◽  
Resin Beads

"De Novo" Sequencing of Peptides Recovered from In-Gel Digested Proteins by Nanoelectrospray Tandem Mass Spectrometry

2002 ◽  
Vol 20 (1) ◽  
pp. 107-118 ◽  
Author(s):  
Andrej Shevchenko ◽  
Igor Chernushevich ◽  
Anna Shevchenko ◽  
Matthias Wilm ◽  
Matthias Mann
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
De Novo ◽  
De Novo Sequencing ◽  
Tandem Mass ◽  
Nanoelectrospray Tandem Mass Spectrometry
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