Antimicrobial peptides from the skin of the Asian frog, Odorrana jingdongensis: De novo sequencing and analysis of tandem mass spectrometry data

2012 ◽  
Vol 75 (18) ◽  
pp. 5807-5821 ◽  
Author(s):  
Jiongyu Liu ◽  
Jianping Jiang ◽  
Zhijun Wu ◽  
Feng Xie
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Antimicrobial Peptides ◽  
De Novo ◽  
De Novo Sequencing ◽  
Mass Spectrometry Data ◽  
Tandem Mass ◽  
Tandem Mass Spectrometry Data

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 XMAn v2—a database of Homo sapiens mutated peptides

2019 ◽  
Author(s):  
Marcela Aguilera Flores ◽  
Iulia M Lazar
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Homo Sapiens ◽  
Amino Acid Sequences ◽  
Mass Spectrometry Data ◽  
Supplementary Information ◽  
Tandem Mass ◽  
Mass Spectrometry Detection ◽  
Nonsense Mutations ◽  
Tandem Mass Spectrometry Data

Abstract Summary The ‘Unknown Mutation Analysis (XMAn)’ database is a compilation of Homo sapiens mutated peptides in FASTA format, that was constructed for facilitating the identification of protein sequence alterations by tandem mass spectrometry detection. The database comprises 2 539 031 non-redundant mutated entries from 17 599 proteins, of which 2 377 103 are missense and 161 928 are nonsense mutations. It can be used in conjunction with search engines that seek the identification of peptide amino acid sequences by matching experimental tandem mass spectrometry data to theoretical sequences from a database. Availability and implementation XMAn v2 can be accessed from github.com/lazarlab/XMAnv2. Supplementary information Supplementary data are available at Bioinformatics online.

Implementation and application of a versatile clustering tool for tandem mass spectrometry data

PROTEOMICS ◽  
2007 ◽  
Vol 7 (18) ◽  
pp. 3245-3258 ◽  
Author(s):  
Kristian Flikka ◽  
Jeroen Meukens ◽  
Kenny Helsens ◽  
Joël Vandekerckhove ◽  
Ingvar Eidhammer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Tandem Mass ◽  
Tandem Mass Spectrometry Data

Correction to Computing Fragmentation Trees from Tandem Mass Spectrometry Data

2011 ◽  
Vol 83 (17) ◽  
pp. 6911-6911
Author(s):  
Florian Rasche ◽  
Aleš Svatoš ◽  
Ravi Kumar Maddula ◽  
Christoph Böttcher ◽  
Sebastian Böcker
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Tandem Mass ◽  
Fragmentation Trees ◽  
Tandem Mass Spectrometry Data
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