De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning

peer-reviewed · Journal of Computational Biology · 2006

peer-reviewed · Journal of Computational Biology · 2006. Marshall Bern et al. We report on a new de novo peptide sequencing algorithm that uses spectral graph partitioning. In this…

Date	2006-03-01
Type	peer-reviewed
Venue	Journal of Computational Biology
Publisher	SAGE Publications
Contribution	algorithm
DOI	10.1089/cmb.2006.13.364
Citations (OpenAlex)	59
Venue 2-year citedness	1.54

Abstract

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 datasets, we outperform the other sequencers. Along with spectral graph theory techniques, the new de novo sequencer 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 dataset.

Authors

Methods and tools

EigenMS: Spectral graph partitioning de novo sequencer with robust TOF mass recalibration.

Cites (15)

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De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004) crossref
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Cited by (26)

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Critical evaluation of the use of artificial data for machine learning based de novo peptide identification (2023) both
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LTQ Orbitrap Velos in routine de novo sequencing of non‐tryptic skin peptides from the frog Rana latastei with traditional and reliable manual spectra interpretation (2016) crossref
Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) both
De Novo Sequencing of Peptides Using Selective 351 nm Ultraviolet Photodissociation Mass Spectrometry (2013) crossref
pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) crossref
Constrained De Novo Sequencing of Conotoxins (2012) both
193 nm Ultraviolet Photodissociation of Imidazolinylated Lys-N Peptides for De Novo Sequencing (2012) crossref
Antilope—A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem (2012) both
Investigation of VUV photodissociation propensities using peptide libraries (2011) both
Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity (2011) both
Constrained De Novo Sequencing of Peptides with Application to Conotoxins (2011) crossref
Algorithm Development of de novo Peptide Sequencing Via Tandem Mass Spectrometry (2010) crossref
TVNovo: De novo peptide sequencing for high resolution LTQ-FT mass spectrometry using virtual database searching (2010) crossref
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Peptide de Novo Sequencing Using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer (2010) crossref
De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation (2009) crossref
Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing (2009) crossref
Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) both
De Novo Sequencing of Nonribosomal Peptides (2008) crossref
De novo peptide identification via mixed-integer linear optimization and tandem mass spectrometry (2008) crossref
Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry (2007) crossref
De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization (2007) crossref
A mixed-integer optimization framework for de novo peptide identification (2007) crossref

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