ArticleJournal of the American Society for Mass Spectrometry2014
Hexicon 2: automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation.
Article in Journal of the American Society for Mass Spectrometry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Integrating protein sequence design and evolutionary sequence conservation to uncover spectral tuning sites in red-light photoreceptors.Structure (London, England : 1993) · 2025Article
- Practical Tips for the Application of HDX-MS to Membrane Proteins, Biomolecular Condensates, and Weak Protein Binders.Journal of the American Society for Mass Spectrometry · 2025Article
- Rigorous Analysis of Multimodal HDX-MS Spectra.Journal of the American Society for Mass Spectrometry · 2025Article
- Computational Tools for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis.Chemical reviews · 2024Review
- Illuminating the inner workings of a natural protein switch: Blue-light sensing in LOV-activated diguanylate cyclases.Science advances · 2023Article
- OligoR: A Native HDX/MS Data Processing Application Dedicated to Oligonucleotides.Analytical chemistry · 2023Article
- Probing Antibody Structures by Hydrogen/Deuterium Exchange Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- Studying Protein-DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes.Life (Basel, Switzerland) · 2020Review
- A small molecule chaperone rescues the stability and activity of a cancer-associated variant of NAD(P)H:quinone oxidoreductase 1 in vitro.FEBS letters · 2020Article
- Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions.Computational and structural biotechnology journal · 2020Review
- deMix: Decoding Deuterated Distributions from Heterogeneous Protein States via HDX-MS.Scientific reports · 2019Article
- Development of Software for the In-Depth Analysis of Protein Dynamics as Determined by MALDI Mass Spectrometry-Based Hydrogen/Deuterium Exchange.Mass spectrometry (Tokyo, Japan) · 2019Article
- Structure-guided design and functional characterization of an artificial red light-regulated guanylate/adenylate cyclase for optogenetic applications.The Journal of biological chemistry · 2018Article
- Article
- Revealing the architecture of protein complexes by an orthogonal approach combining HDXMS, CXMS, and disulfide trapping.Nature protocols · 2018Article
- Long-range allosteric signaling in red light-regulated diguanylyl cyclases.Science advances · 2017Article
- Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope.Journal of the American Society for Mass Spectrometry · 2017Article
- MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets.Bioinformatics (Oxford, England) · 2016Article
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6 authors.
Funding
Abstract
Hydrogen-deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.
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