ArticleJournal of proteome research2013
Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides.
Article in Journal of proteome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 72 citations in OpenAlex.
- Deep coverage and extended sequence reads obtained with a single archaeal protease expedite de novo protein sequencing by mass spectrometry.Cell systems · 2026Article
- XA-Novo: high-throughput mass spectrometry-based de novo sequencing technology for monoclonal antibodies and antibody mixtures.Nature communications · 2026Article
- De Novo Sequencing of Peptides from Tandem Mass Spectra and Applications in Proteogenomics.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
- Origins, Technological Advancement, and Applications of Peptidomics.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Article
- Rapid tryptic peptide mapping of human serum albumin using DI-MS/MSRSC advances · 2022Article
- Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS.Methods (San Diego, Calif.) · 2020Article
- ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping.Molecular & cellular proteomics : MCP · 2020Article
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification.Protein science : a publication of the Protein Society · 2020Review
- Direct Determination of Antibody Chain Pairing by Top-down and Middle-down Mass Spectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation.Analytical chemistry · 2020Article
- PrecisionMolecular & cellular proteomics : MCP · 2019Article
- Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way.Circulation research · 2018Review
- The Role of Electron Transfer Dissociation in Modern Proteomics.Analytical chemistry · 2018Review
- De novo peptide sequencing by deep learning.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom.Scientific data · 2017Article
- Algorithms and design strategies towards automated glycoproteomics analysis.Mass spectrometry reviews · 2017Review
- Implementation of Activated Ion Electron Transfer Dissociation on a Quadrupole-Orbitrap-Linear Ion Trap Hybrid Mass Spectrometer.Analytical chemistry · 2017Article
- Methods, Tools and Current Perspectives in Proteogenomics.Molecular & cellular proteomics : MCP · 2017Review
- Database-independent Protein Sequencing (DiPS) Enables Full-lengthMolecular & cellular proteomics : MCP · 2017Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Full-length de novo sequencing of unknown proteins remains a challenging open problem. Traditional methods that sequence spectra individually are limited by short peptide length, incomplete peptide fragmentation, and ambiguous de novo interpretations. We address these issues by determining consensus sequences for assembled tandem mass (MS/MS) spectra from overlapping peptides (e.g., by using multiple enzymatic digests). We have combined electron-transfer dissociation (ETD) with collision-induced dissociation (CID) and higher-energy collision-induced dissociation (HCD) fragmentation methods to boost interpretation of long, highly charged peptides and take advantage of corroborating b/y/c/z ions in CID/HCD/ETD. Using these strategies, we show that triplet CID/HCD/ETD MS/MS spectra from overlapping peptides yield de novo sequences of average length 70 AA and as long as 200 AA at up to 99% sequencing accuracy.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.