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) | 183 |
| Venue 2-year citedness | 4.69 |
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.
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- HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search (2023) crossref
- Deep Learning Approaches for the Protein Scaffold Filling Problem (2022) crossref
- The Current State-of-the-Art Identification of Unknown Proteins Using Mass Spectrometry Exemplified on De Novo Sequencing of a Venom Protease from Bothrops moojeni (2022) both
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- Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics (2022) semanticscholar
- Metaproteomic Characterization of Forensic Samples (2022) crossref
- Protein cycling in the eastern tropical North Pacific oxygen‐deficient zone: A de novo‐discovery peptidomic approach (2022) crossref
- Database-independent de novo metaproteomics of complex microbial communities (2021) 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
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- Assessing Protein Sequence Database Suitability Using De Novo Sequencing (2020) both
- Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework (2019) both
- Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics (2019) both
- Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome* (2018) crossref
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- Identification, purification, biochemical and mass spectrometric characterization of novel phycobiliproteins from a marine red alga, Centroceras clavulatum (2018) crossref
- Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome (2018) both
- Disentangling thermal stress responses in a reef-calcifier and its photosymbionts by shotgun proteomics (2018) both
- Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries (2017) both
- 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
- Ultrahigh‐resolution Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry for peptide de novo amino acid sequencing for a seven‐protein mixture by paired single‐residue transposed Lys‐N and Lys‐C digestion (2017) crossref
- Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications (2017) crossref
- Rapid Distinction of Leucine and Isoleucine in Monoclonal Antibodies Using Nanoflow LCMSn (2017) crossref
- De novo Peptide Sequencing (2016) 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
- A Proteomic Workflow Using High-Throughput De Novo Sequencing Towards Complementation of Genome Information for Improved Comparative Crop Science (2016) crossref
- Mining Novel Allergens from Coconut Pollen Employing Manual De Novo Sequencing and Homology-Driven Proteomics (2015) crossref
- Using SEQUEST with Theoretically Complete Sequence Databases (2015) both
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) semanticscholar
- Paired single residue‐transposed Lys‐N and Lys‐C digestions for label‐free identification of N‐terminal and C‐terminal MS/MS peptide product ions: ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry for peptide de novo sequencing (2015) crossref
- Characterization of the gila monster (Heloderma suspectum suspectum) venom proteome (2015) both
- Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) both
- De novo identification and quantification of single amino-acid variants in human brain (2014) crossref
- PepExplorer: A Similarity-driven Tool for Analyzing de Novo Sequencing Results (2014) 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