A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry
Ting Chen,Ming-Yang Kao,Matthew Tepel,John Rush,George M. Church +4 more
- pp 389-398
TLDR
The de novo peptide sequencing problem is to reconstruct the peptide sequence from a given tandem mass spectral data of k ions by implicitly transforming the spectral data into an NC-spectrum graph G (V, E) where /V/ = 2k + 2, and this approach can be further used to discover a modified amino acid in O(/V//E/) time.Abstract:
Tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged molecules of prefix and suffix peptide subsequences and then measures mass/charge ratios of ...read more
Citations
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Journal ArticleDOI
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
Bin Ma,Kaizhong Zhang,Christopher Hendrie,Chengzhi Liang,Ming Li,Amanda Doherty-Kirby,Gilles A. Lajoie +6 more
TL;DR: A new de novo sequencing software package, PEAKS, is described, to extract amino acid sequence information without the use of databases, using a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum.
Journal ArticleDOI
Machine learning in bioinformatics
Pedro Larrañaga,Borja Calvo,Roberto Santana,Concha Bielza,Josu Galdiano,Iñaki Inza,Jose A. Lozano,Rubén Armañanzas,Guzmán Santafé,Aritz Pérez,Víctor Robles +10 more
TL;DR: Modelling methods, such as supervised classification, clustering and probabilistic graphical models for knowledge discovery, as well as deterministic and stochastic heuristics for optimization, are presented.
Journal ArticleDOI
De Novo Peptide Sequencing via Tandem Mass Spectrometry
TL;DR: A new algorithm, SHERENGA, is developed for de novo interpretation of MS/MS spectral interpretation that automatically learns fragment ion types and intensity thresholds from a collection of test spectra generated from any type of mass spectrometer.
Journal ArticleDOI
ProLuCID: an improved SEQUEST-like algorithm with enhanced sensitivity and specificity
Tao Xu,Tao Xu,Sung Kyu Park,John D. Venable,James A. Wohlschlegel,Jolene K. Diedrich,Daniel Cociorva,Bingwen Lu,Lujian Liao,J. Hewel,Xuemei Han,Catherine C. L. Wong,Bryan R. Fonslow,Claire M. Delahunty,Yu Gao,H. Shah,John R. Yates +16 more
TL;DR: ProLuCID was able to identify as many as 25% more proteins than SEQUEST and is able to take advantage of high resolution MS/MS spectra leading to further improvements in specificity when compared to low resolution tandem MS data.
Journal ArticleDOI
Spectral Probabilities and Generating Functions of Tandem Mass Spectra: a Strike Against Decoy Databases
TL;DR: It is argued that the generating function approach has the potential to increase the number of peptide identifications in MS/MS searches and the spectral energy/probability approach provides a rigorous solution to the problem of computing statistical significance of spectral identifications.
References
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TL;DR: The updated new edition of the classic Introduction to Algorithms is intended primarily for use in undergraduate or graduate courses in algorithms or data structures and presents a rich variety of algorithms and covers them in considerable depth while making their design and analysis accessible to all levels of readers.
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Journal ArticleDOI
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
TL;DR: The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.
Journal ArticleDOI
De Novo Peptide Sequencing via Tandem Mass Spectrometry
TL;DR: A new algorithm, SHERENGA, is developed for de novo interpretation of MS/MS spectral interpretation that automatically learns fragment ion types and intensity thresholds from a collection of test spectra generated from any type of mass spectrometer.
Book
Proteome Research: New Frontiers in Functional Genomics
TL;DR: The present work focuses on the application of two-Dimensional Electrophoresis to Proteome Modelling and its applications in Clinical and Biomedical Applications of Proteomics.