Lessons in de novo peptide sequencing by tandem mass spectrometry
peer-reviewed · Mass Spectrometry Reviews · 2015
| Date | 2015-01-01 |
| Type | peer-reviewed |
| Venue | Mass Spectrometry Reviews |
| Publisher | Wiley |
| Contribution | review |
| DOI | 10.1002/mas.21406 |
| Citations (OpenAlex) | 211 |
| Venue 2-year citedness | 3.62 |
Abstract
Mass spectrometry has become the method of choice for the qualitative and quantitative characterization of protein mixtures isolated from all kinds of living organisms. The raw data in these studies are MS/MS spectra, usually of peptides produced by proteolytic digestion of a protein. These spectra are “translated” into peptide sequences, normally with the help of various search engines. Data acquisition and interpretation have both been automated, and most researchers look only at the summary of the identifications without ever viewing the underlying raw data used for assignments. Automated analysis of data is essential due to the volume produced. However, being familiar with the finer intricacies of peptide fragmentation processes, and experiencing the difficulties of manual data interpretation allow a researcher to be able to more critically evaluate key results, particularly because there are many known rules of peptide fragmentation that are not incorporated into search engine scoring. Since the most commonly used MS/MS activation method is collision-induced dissociation (CID), in this article we present a brief review of the history of peptide CID analysis. Next, we provide a detailed tutorial on how to determine peptide sequences from CID data. Although the focus of the tutorial is de novo sequencing, the lessons learned and resources supplied are useful for data interpretation in general.
Methods and tools
- Lessons in de novo peptide sequencing: Mass Spectrometry Reviews tutorial/review on lessons in de novo peptide sequencing by tandem mass spectrometry.
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- Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides (2025) crossref
- Framework for de novo sequencing of peptide mixtures via network analysis and two-dimensional tandem mass spectrometry (2025) crossref
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- The Hunt Lab Guide to De Novo Peptide Sequence Analysis by Tandem Mass Spectrometry (2024) both
- De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments (2023) both
- Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review (2023) crossref
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- Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics (2022) both
- Metaproteomic Characterization of Forensic Samples (2022) crossref
- 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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- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines (2018) crossref
- Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation (2017) both