Divergent Antibody Repertoires Found for Omicron versus Wuhan SARS-CoV-2 Strains Using Ig-MS

Forte, Eleonora; Soye, Benjamin J. Des; Melani, Rafael D.; Hollas, Michael A.; Kafader, Jared O.; Sha, Beverly E.; Schneider, John C.; Kelleher, Neil L.

doi:10.1021/acs.jproteome.2c00514

Cited by 4 publications

(1 citation statement)

References 57 publications

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“…Another TDP challenge is the overlapping of different species, charge states and isotopic distributions in the limited m/z space of mass spectra. To address this, Kafader et al developed Individual Ion Mass Spectrometry (I 2 MS) that was recently used for analyzing antibody repertoires against SARS-CoV-2 in COVID-19 patients and vaccinated individuals ( 97 – 99 ).…”

Section: Top-down Proteomics In Transplantation: the Move From Protei...mentioning

confidence: 99%

Mass spectrometry-based proteomics for advancing solid organ transplantation research

Huang,

Su,

Fisher

et al. 2023

Front. Transplant.

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Scarcity of high-quality organs, suboptimal organ quality assessment, unsatisfactory pre-implantation procedures, and poor long-term organ and patient survival are the main challenges currently faced by the solid organ transplant (SOT) field. New biomarkers for assessing graft quality pre-implantation, detecting, and predicting graft injury, rejection, dysfunction, and survival are critical to provide clinicians with invaluable prediction tools and guidance for personalized patients' treatment. Additionally, new therapeutic targets are also needed to reduce injury and rejection and improve transplant outcomes. Proteins, which underlie phenotypes, are ideal candidate biomarkers of health and disease statuses and therapeutic targets. A protein can exist in different molecular forms, called proteoforms. As the function of a protein depends on its exact composition, proteoforms can offer a more accurate basis for connection to complex phenotypes than protein from which they derive. Mass spectrometry-based proteomics has been largely used in SOT research for identification of candidate biomarkers and therapeutic intervention targets by so-called “bottom-up” proteomics (BUP). However, such BUP approaches analyze small peptides in lieu of intact proteins and provide incomplete information on the exact molecular composition of the proteins of interest. In contrast, “Top-down” proteomics (TDP), which analyze intact proteins retaining proteoform-level information, have been only recently adopted in transplantation studies and already led to the identification of promising proteoforms as biomarkers for organ rejection and dysfunction. We anticipate that the use of top-down strategies in combination with new technological advancements in single-cell and spatial proteomics could drive future breakthroughs in biomarker and therapeutic target discovery in SOT.

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Section: Top-down Proteomics In Transplantation: the Move From Protei...mentioning

confidence: 99%

Mass spectrometry-based proteomics for advancing solid organ transplantation research

Huang,

Su,

Fisher

et al. 2023

Front. Transplant.

Self Cite

View full text Add to dashboard Cite

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Mass spectrometry characterization of antibodies at the intact and subunit levels: From targeted to large-scale analysis

Kline,

Melani,

Fornelli

2023

International Journal of Mass Spectrometry

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Automated Immunoprecipitation, Sample Preparation, and Individual Ion Mass Spectrometry Platform for Proteoforms

Des Soye,

McGee,

Hollas

et al. 2024

Anal. Chem.

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Charge detection mass spectrometry (CDMS) is a well-established technique that provides direct mass spectral outputs regardless of analyte heterogeneity or molecular weight. Over the past few years, it has been demonstrated that CDMS can be multiplexed on Orbitrap analyzers utilizing an integrated approach termed individual ion mass spectrometry (I2MS). To further increase adaptability, robustness, and throughput of this technique, here, we present a method that utilizes numerous integrated equipment components including a Kingfisher system, SampleStream platform, and Q Exactive mass spectrometer to provide a fully automated workflow for immunoprecipitation, sample preparation, injection, and subsequent I2MS acquisition. This automated workflow has been applied to a cohort of 58 test subjects to determine individualized patient antibody responses to SARS-CoV-2 antigens. Results from a range of serum donors include 37 subject I2MS spectra that contained a positive COVID-19 antibody response and 21 I2MS spectra that contained a negative COVID-19 antibody response. This high-throughput automated I2MS workflow can currently process over 100 samples per week and is general for making immunoprecipitation-MS workflows achieve proteoform resolution.

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Divergent Antibody Repertoires Found for Omicron versus Wuhan SARS-CoV-2 Strains Using Ig-MS

Cited by 4 publications

References 57 publications

Mass spectrometry-based proteomics for advancing solid organ transplantation research

Mass spectrometry-based proteomics for advancing solid organ transplantation research

Mass spectrometry characterization of antibodies at the intact and subunit levels: From targeted to large-scale analysis

Automated Immunoprecipitation, Sample Preparation, and Individual Ion Mass Spectrometry Platform for Proteoforms

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