De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation

peer-reviewed · Analytical Chemistry · 2004

peer-reviewed · Analytical Chemistry · 2004. Zhongqi Zhang. Mass spectrometry-based de novo peptide sequencing is generally more reliable on high-resolution instruments…

Date	2004-09-15
Type	peer-reviewed
Venue	Analytical Chemistry
Publisher	American Chemical Society (ACS)
Contribution	algorithm
DOI	10.1021/ac0491206
Citations (OpenAlex)	75
Venue 2-year citedness	7.10

Abstract

Mass spectrometry-based de novo peptide sequencing is generally more reliable on high-resolution instruments owing to their high resolution and mass accuracy. On a lower resolution instrument such as the more widely used quadrupole ion traps, de novo peptide sequencing is not so reliable or requires more MS(3) experiments. However, the peptide CID spectrum has been demonstrated to be quite reproducible on an ion trap instrument and can be predicted with good accuracy. A new de novo peptide sequencing technique, DACSIM, combining a divide-and-conquer algorithm for deriving sequence candidates and spectrum simulation for sequence refinement, is developed for spectra acquired on an ion trap instrument. When DACSIM was used to sequence peptides 500-1900 u in mass generated from proteolytic digests of hemoglobin and myoglobin, the success rate was 70% with a false positive rate of only 6%, when isoleucine and leucine residues were not distinguished.

Authors

Zhongqi Zhang · Amgen Inc.

Methods and tools

DC-Novo: Divide-and-conquer + spectrum simulation

Cites (10)

Cited by (25)

PepGo: a deep learning and tree search-based model for de novo peptide sequencing (2025) crossref
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing (2025) crossref
De Novo Sequencing of Peptides from Tandem Mass Spectra and Applications in Proteogenomics (2024) crossref
Lys-Sequencer: An algorithm for de novo sequencing of peptides by paired single residue transposed Lys-C and Lys-N digestion coupled with high-resolution mass spectrometry (2020) crossref
A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
De novo peptide sequencing by deep learning (2017) crossref
Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
De novo Peptide Sequencing (2016) crossref
Peptide de novo sequencing of mixture tandem mass spectra (2016) both
Novor: Real-Time Peptide de Novo Sequencing Software (2015) both
De Novo Sequencing of Peptides Using Selective 351 nm Ultraviolet Photodissociation Mass Spectrometry (2013) crossref
193 nm Ultraviolet Photodissociation of Imidazolinylated Lys-N Peptides for De Novo Sequencing (2012) crossref
De Novo Sequencing and Homology Searching (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
Algorithm Development of de novo Peptide Sequencing Via Tandem Mass Spectrometry (2010) crossref
ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010) crossref
De NovoSequencing of Tryptic Peptides Derived fromDeinococcus radioduransRibosomal Proteins Using 157 nm Photodissociation MALDI TOF/TOF Mass Spectrometry (2010) crossref
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
Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) both
A mixed-integer optimization framework for de novo peptide identification (2007) crossref
De novo peptide sequencing using exhaustive enumeration of peptide composition (2006) crossref
De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning (2006) crossref

Seen in the charts

Back to the full map