Novor: Real-Time Peptide de Novo Sequencing Software

peer-reviewed · Journal of the American Society for Mass Spectrometry · 2015

peer-reviewed · Journal of the American Society for Mass Spectrometry · 2015. Bin Ma. De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass…

Date	2015-06-30
Type	peer-reviewed
Venue	Journal of the American Society for Mass Spectrometry
Publisher	American Chemical Society (ACS)
Contribution	algorithm
DOI	10.1007/s13361-015-1204-0
Citations (OpenAlex)	263
Venue 2-year citedness	2.84

Abstract

De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today’s peptide de novo sequencing analyses. To improve the accuracy, Novor’s scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%-37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today’s mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data. Graphical Abstract ᅟ.

Authors

Bin Ma · Rapid Novor Inc., University of Waterloo, University of Western Ontario, Western University

Methods and tools

Novor: Real-time decision-tree scoring

Data used

BioID-based identification of SCF-BTrCP1/2 E3 ligase substrates (as deposited) · MSV000078991
Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative p (as deposited) · PXD001220

Cites (24)

De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra (2014) both
UniNovo: a universal tool for de novo peptide sequencing (2013) both
DE NOVO SEQUENCING WITH LIMITED NUMBER OF POST-TRANSLATIONAL MODIFICATIONS PER PEPTIDE (2013) both
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2012) semanticscholar
De Novo Sequencing and Homology Searching (2012) semanticscholar
ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010) both
pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) both
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy (2009) both
A comparative study of the accuracy of several de novo sequencing software packages for datasets derived by matrix‐assisted laser desorption/ionisation and electrospray (2008) both
Isolation and Characterization of Carnocyclin A, a Novel Circular Bacteriocin Produced by Carnobacterium maltaromaticum UAL307 (2008) both
Proteome Analysis of Pitcher Fluid of the Carnivorous Plant Nepenthes alata (2008) both
MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) both
De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization (2007) both
Performance Evaluation of Existing De Novo Sequencing Algorithms (2006) both
NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing (2005) both
Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry (2005) crossref
InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra (2005) both
An effective algorithm for peptide de novo sequencing from MS/MS spectra (2005) both
PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004) both
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) both
De novo peptide sequencing via tandem mass spectrometry (1999) both
Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997) both

Cited by (137)

Cited in patents (3)

US11573239B2 Methods and systems for de novo peptide sequencing using deep learning ↗ (Bioinformatics Solutions Inc., priority 2017-07-17, active)
US11694769B2 Systems and methods for de novo peptide sequencing from data-independent acquisition using deep learning ↗ (Bioinformatics Solutions Inc., priority 2017-07-17, active)
US12340874B1 Artificial neural network models for prediction of de novo sequencing of chains of amino acids ↗ (Verily Life Sciences, priority 2017-11-03, active)

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