Gábor Transform-Based Signal Isolation, Rapid Deconvolution, and Quantitation of Intact Protein Ions with Mass Spectrometry.

High-resolution mass spectrometry (HRMS) is a powerful technique for the characterization and quantitation of complex biological mixtures, with several applications including clinical monitoring and tissue imaging. However, these medical and pharmaceutical applications are pushing the analytical limits of modern HRMS techniques, requiring either further development in instrumentation or data processing methods. Here, we demonstrate new developments in the interactive Fourier-transform analysis for mass spectrometry (iFAMS) software including the first application of Gábor transform (GT) to protein quantitation. Newly added automation tools detect signals from minimal user input and apply thresholds for signal selection, deconvolution, and baseline correction to improve the objectivity and reproducibility of deconvolution. Additional tools were added to improve the deconvolution of highly complex or congested mass spectra and are demonstrated here for the first time. The "Gábor Slicer" enables the user to explore trends in the Gábor spectrogram with instantaneous ion mass estimates accurate to 10 Da. The charge adjuster allows for easy visual confirmation of accurate charge state assignments and quick adjustment if necessary. Deconvolution refinement utilizes a second GT of isotopically resolved data to remove common deconvolution artifacts. To assess the quality of deconvolution from iFAMS, several comparisons are made to deconvolutions using other algorithms such as UniDec and an implementation of MaxEnt in Agilent MassHunter BioConfirm. Lastly, the newly added batch processing and quantitation capabilities of iFAMS are demonstrated and compared to a common extracted ion chromatogram approach.

Gábor Transform-Based Antibody Quantitation in Serum: An Interlaboratory Liquid Chromatography/High-Resolution Mass Spectrometry Investigation.

Therapeutic monoclonal antibodies (t-mAbs) are crucial for treating various conditions, including cancers and autoimmune disorders. Accurate quantitation and pharmacokinetic monitoring of t-mAbs in serum are essential, but current methods like ligand binding assays (LBAs) and bottom-up peptide liquid chromatography-tandem mass spectrometry (LC-MS/MS) can lack the sensitivity and specificity needed to meet clinical demands. Emerging techniques using high-resolution mass spectrometry (HRMS) in top-down and middle-up approaches offer improved ability to accurately quantify mAb proteoforms apart from degradation products by keeping the sample proteins intact or minimizing digestion. This study describes the first use of Gábor transform (GT)-based iFAMS Quant+ software to quantify a t-mAb (vedolizumab) from ∼400 samples using an Agilent 6545XT AdvanceBio Q-TOF at the University of Oregon. These results are compared to a previously validated laboratory-developed test (LDT) from Mayo Clinic utilizing a Thermo Q Exactive Plus Orbitrap. The Mayo method used conventional extracted ion chromatograms (XICs) of select charge states for quantitation, while the iFAMS Quant+ method utilized GT-based charge state deconvolution, background subtraction, and signal integration. Calibration and quality control (QC) analyses and Passing-Bablok regression of 351 subject samples demonstrated excellent agreement between the two methods. The iFAMS Quant+ workflow exhibited unique advantages for characterizing interferents and analyte signal anomalies due to its deconvolution-based approach.

Identification of a monoclonal antibody clipping variant by cross-validation using capillary electrophoresis - sodium dodecyl sulfate, capillary zone electrophoresis - mass spectrometry and capillary isoelectric focusing - mass spectrometry.

Critical quality attributes (CQAs) of recombinant monoclonal antibody therapeutics are constantly monitored throughout the life cycle of drug development and manufacturing. In the past few decades, numerous analytical techniques have been developed for the characterization of CQAs. In this regard, non-reduced and reduced capillary electrophoresis - sodium dodecyl sulfate (CE-SDS) methods have been widely adopted by the biopharmaceutical industry for the evaluation of size-related heterogeneities in biologics. In this work we demonstrate that, with recent development of capillary electrophoresis - mass spectrometry (CE-MS) technologies, a clipping variant of bevacizumab may be identified directly by both capillary zone electrophoresis - mass spectrometry (CZE-MS) and capillary isoelectric focusing - mass spectrometry (cIEF-MS) approaches, providing a powerful addition to the traditional CE-SDS analysis workflow. In this novel workflow, linear regression between the mobility and molecular weight first results in an approximate size range of this variant. The intact masses of all species in the bevacizumab are then obtained, after deconvolution of all features identified in the CZE-MS analysis. Subsequent  CZE-MS analysis of the subunits of bevacizumab leads to the confirmation of a clipped heavy chain. Furthermore, cIEF-MS of the intact bevacizumab confirms the existence of this clipping variant. The cross-validation between CE-SDS, CZE-MS, and cIEF-MS, creates a comprehensive roadmap for monoclonal antibody size variants profiling. These CE-based analytical techniques are complementary to each other, leading to orthogonal verification for size heterogeneity characterization.

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids.

Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with high reproducibility (CV 6 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. This SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure.