De Novo Sequencing and Homology Searching
peer-reviewed · Molecular & Cellular Proteomics · 2012
peer-reviewed · Molecular & Cellular Proteomics · 2012. Bin Ma et al. In proteomics, de novo sequencing is the process of deriving peptide sequences from tandem mass spectra…
| Date | 2012-02-01 |
| Type | peer-reviewed |
| Venue | Molecular & Cellular Proteomics |
| Publisher | Elsevier BV |
| Contribution | review |
| DOI | 10.1074/mcp.O111.014902 |
| Citations (OpenAlex) | 188 |
| Venue 2-year citedness | 4.17 |
Abstract
In proteomics, de novo sequencing is the process of deriving peptide sequences from tandem mass spectra without the assistance of a sequence database. Such analyses have traditionally been performed manually by human experts, and more recently by computer programs that have been developed because of the need for higher throughput. Although powerful, de novo sequencing often can only determine partially correct sequence tags because of imperfect tandem mass spectra. However, these sequence tags can then be searched in a sequence database to identify the exact or a homologous peptide. Homology searches are particularly useful for the study of organisms whose genomes have not been sequenced. This tutorial will present background important to understanding de novo sequencing, suggestions on how to do this manually, plus descriptions of computer algorithms used to automate this process and to subsequently carryout homology-based database searches. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 1).
Methods and tools
- De novo sequencing and homology searching: Molecular & Cellular Proteomics review/tutorial on de novo sequencing and homology searching.
Cites (25)
- ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010) both
- Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR (2010) both
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) both
- A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry (2010) both
- De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation (2009) both
- Automated de novo protein sequencing of monoclonal antibodies (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
- AUDENS: A Tool for Automated Peptide de Novo Sequencing (2005) both
- SPIDER: software for protein identification from sequence tags with de novo sequencing error (2005) crossref
- 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
- Shotgun Protein Sequencing by Tandem Mass Spectra Assembly (2004) both
- De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004) both
- GutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model (2003) both
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001) both
- 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
- Rapid de novo peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer (1997) both
- Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997) both
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) both
- Computer program (SEQPEP) to aid in the interpretation of high-energy collision tandem mass spectra of peptides (1989) both
Cited by (20)
- Limitations of de novo sequencing in resolving sequence ambiguity (2025) crossref
- Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing (2025) crossref
- Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review (2023) crossref
- Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics (2022) semanticscholar
- Metaproteomic Characterization of Forensic Samples (2022) crossref
- De novo sequencing of proteins by mass spectrometry (2020) both
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification (2020) crossref
- Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework (2019) both
- 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
- Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation (2017) both
- NIPTL-Novo: Non-isobaric peptide termini labeling assisted peptide de novo sequencing (2017) crossref
- Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications (2017) crossref
- UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry (2016) both
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) semanticscholar
- Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) both
- UniNovo: a universal tool for de novo peptide sequencing (2013) both
- High-Confidence de Novo Peptide Sequencing Using Positive Charge Derivatization and Tandem MS Spectra Merging (2013) crossref
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) crossref
- Mass spectrometry-based protein identification by integrating de novo sequencing with database searching (2013) both