Data on crystal organization in the structure of the Fab fragment from the NIST reference antibody, RM 8671

Gallagher, D.T.; Karageorgos, Ioannis; Hudgens, Jeffrey W.; Galvin, Connor

doi:10.1016/j.dib.2017.11.013

Cited by 12 publications

(12 citation statements)

References 6 publications

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“…Study Design and Protocols. During the NIST interlaboratory HDX-MS study, each laboratory received a standardized kit that contained buffered solution of Fab fragment of NISTmAb reference material (PDB: 5K8A), ( Marino et al, 2015 ; Karageorgos et al, 2017 ; Gallagher et al, 2018 ), and vials of buffers and reagents used during the sample labeling, sample denaturing, and quenching steps ( Figure 5 ). The kit harmonized solution pH, salt concentration and disulfide bond reducing power.…”

Section: Hydrogen-deuterium Exchange Mass Spectrometry Interlaborator...mentioning

confidence: 99%

Interlaboratory Studies Using the NISTmAb to Advance Biopharmaceutical Structural Analytics

Yandrofski

Mouchahoir

Leoz

et al. 2022

Front. Mol. Biosci.

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Biopharmaceuticals such as monoclonal antibodies are required to be rigorously characterized using a wide range of analytical methods. Various material properties must be characterized and well controlled to assure that clinically relevant features and critical quality attributes are maintained. A thorough understanding of analytical method performance metrics, particularly emerging methods designed to address measurement gaps, is required to assure methods are appropriate for their intended use in assuring drug safety, stability, and functional activity. To this end, a series of interlaboratory studies have been conducted using NISTmAb, a biopharmaceutical-representative and publicly available monoclonal antibody test material, to report on state-of-the-art method performance, harmonize best practices, and inform on potential gaps in the analytical measurement infrastructure. Reported here is a summary of the study designs, results, and future perspectives revealed from these interlaboratory studies which focused on primary structure, post-translational modifications, and higher order structure measurements currently employed during biopharmaceutical development.

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Section: Hydrogen-deuterium Exchange Mass Spectrometry Interlaborator...mentioning

confidence: 99%

Interlaboratory Studies Using the NISTmAb to Advance Biopharmaceutical Structural Analytics

Yandrofski

Mouchahoir

Leoz

et al. 2022

Front. Mol. Biosci.

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“…The deuterium content of peptic peptide fragments were measured by mass spectrometry. [1][2][3] These data were reported by fifteen laboratories, which conducted the measurements using orbitrap and Q-TOF mass spectrometers. The cohort reported ≈ 78,900 centroids for 430 proteolytic peptide sequences of the heavy and light chains of NISTmAb, providing nearly 100 % coverage.…”

Section: Discussionmentioning

confidence: 99%

“…Each laboratory conducted proteomics studies on the Fab fragment of NISTmAb (PDB: 5K8A) [1][2][3] and performed three HDX-MS runs. Here, the term "run" is defined by the procedures and capabilities of the laboratory equipment.…”

Section: Bottom-up Hdx-ms Measurementsmentioning

confidence: 99%

“…The test protein for the HDX-MS interlaboratory comparison was the Fab fragment that is enzymatically cleaved from Candidate RM 8670 (Lot #5F1b), which has the same structure as the Fab of the NIST IgG1κ reference material, NISTmAb RM8671. [1][2][3] Material used for this study contained a small fraction of free Fc fragment. Triple-angle light scattering data indicated that the Fab fragment of NISTmAb sample was in a monomeric state [2,3].…”

Section: Reagents and Materialsmentioning

confidence: 99%

“…[1][2][3] Material used for this study contained a small fraction of free Fc fragment. Triple-angle light scattering data indicated that the Fab fragment of NISTmAb sample was in a monomeric state [2,3]. Testing showed that the protein is unaltered by the mechanical shocks associated with shipping [2].…”

Section: Reagents and Materialsmentioning

confidence: 99%

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Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Centroid Data Measured between 3.6 °C and 25.4 °C for the Fab Fragment of NISTmAb

Hudgens

Gallagher

Karageorgos

et al. 2019

J. RES. NATL. INST. STAN.

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The spreadsheet file reported herein provides centroid data, descriptive of deuterium uptake, for the FabFragment of NISTmAb (PDB: 5K8A) reference material, as measured by the bottom-up hydrogen-deuterium exchange mass spectrometry (HDX-MS) method. The protein sample was incubated in deuterium-rich solutions under uniform pH and salt concentrations between 3.6 oC and 25.4 oC for seven intervals ranging over (0 to 14,400) s plus a ∞pseudo s control. The deuterium content of peptic peptide fragments were measured by mass spectrometry. These data were reported by fifteen laboratories, which conducted the measurements using orbitrap and Q-TOF mass spectrometers. The cohort reported ≈ 78,900 centroids for 430 proteolytic peptide sequences of the heavy and light chains of NISTmAb, providing nearly 100 % coverage. In addition, some groups reported ≈ 10,900 centroid measurements for 77 peptide sequences of the Fc fragment. The instrumentation and physical and chemical conditions under which these data were acquired are documented.

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Two‐Dimensional Correlation and Two‐Dimensional Co‐Distribution Spectroscopies of Proteins

Pastrana¹,

Meuse²

2022

Encyclopedia of Analytical Chemistry

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Given the complexity of proteins, the broad nature of infrared bands, and the overlap of the HOH bending mode of water within the 1700–1600 cm −1 spectral region, it was often considered too difficult to include side‐chain vibrational modes in a description of a protein's dynamic behavior in solution. Yet, it is the roles of side‐chains that allow a description of a protein's dynamics to become a site‐specific understanding of stability and provide a basis for the development of protein drugs. This article describes how, in certain cases, site‐specific analysis of protein infrared spectra can be performed using two‐dimensional infrared correlation spectroscopy ( 2D‐COS ) developed by Dr. Isao Noda. The 2D‐COS algorithm spreads overlapped peaks within a spectral region of interest into a second dimension that allows for a complete evaluation of all of the peaks that change during a perturbation. 2D‐COS analysis has been implemented successfully for the study of proteins under different perturbations such as pressure, chemical, pH, concentration, and most commonly temperature. Initially, the interest was in determining conformational changes during thermal unfolding, which then led to evaluating solvent accessibility through hydrogen/deuterium exchange, leading to the use of isotope editing to probe local structural changes and interactions. Herein, we will explore the extent that both 2D‐COS and two‐dimensional co‐distribution spectroscopy ( 2D‐CDS ) have been implemented in the study of proteins. However, we were also keen to include recent advances to site‐specifically monitor protein deamidation in aqueous solution. Protein deamidation, like oxidation and glycosylation, is one of the processes that can initiate protein degradation pathways which could lead to decreased target binding, decreased stability, and possibly aggregation. These concerns have become part of the critical quality attributes ( CQAs ) evaluated during therapeutic protein development because they can potentially impact drug safety and efficacy. To date, tandem liquid chromatography–mass spectrometry ( LC‐MS ) techniques have been the primary method used to ascertain the presence and sites of deamidation in protein samples. However, the LC‐MS process requires multiple steps, including enzymatic digestion and peptide mapping. 2D‐COS and 2D‐CDS analyses provide an alternative that allows the determination of the deamidation sites and the evaluation of the stability of the protein populations within a sample without any sample preparation steps. The 2D‐COS method utilizes an innovative platform comprised of a quantum cascade laser microscope ( QCLM ), slide cell array, and software. The QCLM provides an enhanced signal/noise ratio and real‐time acquisition of hyperspectral images of an array of proteins in solution under accurate thermal control. The method monitors the deamidation process during thermal stress. Spectral data is then subject to 2D‐COS analysis to determine the extent of and site at which both asparagine and glutamine deamidation occur. In addition, 2D‐CDS analysis allows assessment of changes in stability in the distributions of the protein populations during the perturbation. The results presented here for the deamidation of the NISTmAb have been validated by LC‐MS to evaluate this new analytical tool. We foresee this approach as a required step in a therapeutic protein's developability assessment and release testing.

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Data on crystal organization in the structure of the Fab fragment from the NIST reference antibody, RM 8671

Cited by 12 publications

References 6 publications

Interlaboratory Studies Using the NISTmAb to Advance Biopharmaceutical Structural Analytics

Interlaboratory Studies Using the NISTmAb to Advance Biopharmaceutical Structural Analytics

Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Centroid Data Measured between 3.6 °C and 25.4 °C for the Fab Fragment of NISTmAb

Two‐Dimensional Correlation and Two‐Dimensional Co‐Distribution Spectroscopies of Proteins

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