Dataset Information

Tracking genome-editing and associated molecular perturbations by SWATH mass spectrometry

ABSTRACT: Advances in gene editing now allow reverse genetics to be applied to a broad range of biological systems. Ultimately, any modification to coding sequences requires confirmation at the protein level, although immunoblotting is often hampered by antibody quality or availability especially in non-mammalian species. Here, we show that Sequential Window Acquisition of All Theoretical Spectra (SWATH) - Mass Spectrometry (MS) is a robust antibody-independent alternative for monitoring gene editing at the protein level and concomitantly defines proteome responses which may provide pertinent biological insights.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Bicyclus Anynana Danio Rerio (zebrafish) (brachydanio Rerio) Mus Musculus (mouse)

TISSUE(S): Pupa, Embryo, Tail Fin, Cell Culture

SUBMITTER: Qifeng Lin

LAB HEAD: Jayantha Gunaratne

PROVIDER: PXD013176 | Pride | 2019-10-24

REPOSITORIES: Pride

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Publications

Tracking genome-editing and associated molecular perturbations by SWATH mass spectrometry.

Lin Qifeng Q Low Larry W L LWL Lau Adam A Chua Esther W L EWL Matsuoka Yuji Y Lian Yilong Y Monteiro Antónia A Tate Stephen S Gunaratne Jayantha J Carney Tom J TJ

Scientific reports 20191023 1

Advances in gene editing now allow reverse genetics to be applied to a broad range of biological systems. Ultimately, any modification to coding sequences requires confirmation at the protein level, although immunoblotting is often hampered by antibody quality or availability especially in non-model species. Sequential Window Acquisition of All Theoretical Spectra (SWATH), a mass spectrometry (MS) technology with exceptional quantitative reproducibility and accuracy, offers an ideal alternative ...[more]

PMID: 31645615

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Project description:In the last two years, the coronavirus disease 19 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a scientific and social challenge worldwide. Vaccines have been the most effective intervention for reducing virus transmission and disease severity. However, virus genetic variants are still circulating among vaccinated individuals with different symptomatology disease cases. Understanding the protective or disease associated mechanisms in vaccinated individuals is relevant to advance in vaccine development and implementation. To address this objective, serum protein profiles were characterized by quantitative proteomics and data analysis algorithms in four cohorts of vaccinated individuals uninfected and SARS-CoV-2 infected with asymptomatic, nonsevere and severe disease symptomatology. The results showed that immunoglobulins were the most overrepresented proteins in infected cohorts when compared to PCR-negative individuals. The immunoglobulin profile varied between different infected cohorts and correlated with protective or disease associated capacity. Overrepresented immunoglobulins in PCR-positive individuals correlated with protective response against SARS-CoV-2, other viruses, and thrombosis in asymptomatic cases. In nonsevere cases, correlates of protection against SARS-CoV-2 and HBV together with risk of myasthenia gravis and allergy and autoantibodies were observed. Patients with severe symptoms presented risk for allergy, chronic idiopathic thrombocytopenic purpura, and autoantibodies. The analysis of underrepresented immunoglobulins in PCR-positive compared to PCR-negative individuals identified vaccine-induced protective epitopes in various coronavirus proteins including the Spike receptor-binding domain RBD. Non-immunoglobulin proteins were associated with COVID-19 symptoms and biological processes. These results evidence host-associated differences in response to vaccination and the possibility of improving vaccine efficacy against SARS-CoV-2.

Dataset Information

Tracking genome-editing and associated molecular perturbations by SWATH mass spectrometry

Publications

Tracking genome-editing and associated molecular perturbations by SWATH mass spectrometry.

Similar Datasets

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