Robust regression and outlier detection
Robust regression and outlier detection
Matrix computations (3rd ed.)
Spectral partitioning with multiple eigenvectors
Discrete Applied Mathematics - Special volume on VLSI
Normalized Cuts and Image Segmentation
IEEE Transactions on Pattern Analysis and Machine Intelligence
On de novo interpretation of tandem mass spectra for peptide identification
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Separation of Ion Types in Tandem Mass Spectrometry Data Interpretation " A Graph-Theoretic Approach
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
PPM-Chain De novo Peptide Identification Program Comparable in Performance to Sequest
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Automatic Quality Assessment of Peptide Tandem Mass Spectra
Bioinformatics
An effective algorithm for the peptide de novo sequencing from MS/MS spectrum
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Combinatorial Approaches for Mass Spectra Recalibration
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A new approach to protein identification
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
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We report on a new de novo peptide sequencing algorithm that uses spectral graph partitioning. In this approach, relationships between m/z peaks are represented by attractive and repulsive springs, and the vibrational modes of the spring system are used to infer information about the peaks (such as “likely b-ion” or “likely y-ion”). We demonstrate the effectiveness of this approach by comparison with other de novo sequencers on test sets of ion-trap and QTOF spectra, including spectra of mixtures of peptides. On all data sets we outperform the other sequencers. Along with spectral graph theory techniques, EigenMS incorporates another improvement of independent interest: robust statistical methods for recalibration of time-of-flight mass measurements. Robust recalibration greatly outperforms simple least-squares recalibration, achieving about three times the accuracy for one QTOF data set.