HDXfit

HDXfit fits site-specific amide hydrogen/deuterium exchange probabilities to peptide mass envelopes from hydrogen/deuterium exchange (HX) mass spectrometry (MS) data to resolve residue-specific exchange information for protein structural and biophysical characterization.

Key Features:

• Site-Resolved Analysis: Integrates isotopic envelope-shape information to infer residue-specific amide exchange probabilities from peptide mass envelopes.
• Iterative Optimization (HDsite): Applies an iterative optimization program (HDsite) to estimate site-level exchange and perform back-exchange corrections.
• Comparative Fitting Methods: Implements least squares and multinomial distribution fitting of isotopic envelope intensities, with reported superior precision for least squares on envelope data.
• Analytical Optimization: Uses exact expressions for the gradient and Hessian of the objective function together with a trust-region algorithm in compact analytical form for robust parameter optimization.
• Envelope Deconvolution and Error Sensitivity: Incorporates envelope deconvolution to refine fits and accounts for sensitivity of deuterium distributions to experimental errors and peptide arrangements.

Scientific Applications:

• Residue-specific protein dynamics: Enables analysis of hydrogen/deuterium exchange at the amino-acid level to inform on protein conformational dynamics and function.
• Protein structural and biophysical characterization: Supports characterization of large biologically important proteins where traditional HX MS resolution or material constraints limit residue-level interpretation.

Methodology:

Fits site-specific amide exchange probabilities to peptide isotopic envelopes using least squares and multinomial distribution fitting, employs exact gradient and Hessian expressions with a trust-region algorithm for optimization, uses the iterative HDsite program for back-exchange corrections, applies envelope deconvolution to refine fits, and validates results against hydrogen exchange NMR measurements and simulation trials.