scholarly journals Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics

2020 ◽  
Vol 21 (4) ◽  
pp. 1524 ◽  
Author(s):  
Van-An Duong ◽  
Jong-Moon Park ◽  
Hookeun Lee
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
State Of The Art ◽  
Three Dimensional ◽  
Early Period ◽  
Proteome Analysis ◽  
High Sensitivity ◽  
Sample Complexity ◽  
Multidimensional Separations

Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.

scholarly journals Characterization of Polycaprolactone Nanohydroxyapatite Composites with Tunable Degradability Suitable for Indirect Printing

Polymers ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 295
Author(s):  
Stephanie E. Doyle ◽  
Lauren Henry ◽  
Ellen McGennisken ◽  
Carmine Onofrillo ◽  
Claudia Di Bella ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Large Scale ◽  
Three Dimensional ◽  
Cell Number ◽  
Compressive Modulus ◽  
Degradation Rates ◽  
Scaffold Materials ◽  
Natural Tissue ◽  
Complete Regeneration

Degradable bone implants are designed to foster the complete regeneration of natural tissue after large-scale loss trauma. Polycaprolactone (PCL) and hydroxyapatite (HA) composites are promising scaffold materials with superior mechanical and osteoinductive properties compared to the single materials. However, producing three-dimensional (3D) structures with high HA content as well as tuneable degradability remains a challenge. To address this issue and create homogeneously distributed PCL-nanoHA (nHA) scaffolds with tuneable degradation rates through both PCL molecular weight and nHA concentration, we conducted a detailed characterisation and comparison of a range of PCL-nHA composites across three molecular weight PCLs (14, 45, and 80 kDa) and with nHA content up to 30% w/w. In general, the addition of nHA results in an increase of viscosity for the PCL-nHA composites but has little effect on their compressive modulus. Importantly, we observe that the addition of nHA increases the rate of degradation compared to PCL alone. We show that the 45 and 80 kDa PCL-nHA groups can be fabricated via indirect 3D printing and have homogenously distributed nHA even after fabrication. Finally, the cytocompatibility of the composite materials is evaluated for the 45 and 80 kDa groups, with the results showing no significant change in cell number compared to the control. In conclusion, our analyses unveil several features that are crucial for processing the composite material into a tissue engineered implant.

scholarly journals State-of-the-Art Native Mass Spectrometry and Ion Mobility Methods to Monitor Homogeneous Site-Specific Antibody-Drug Conjugates Synthesis

2021 ◽  
Vol 14 (6) ◽  
pp. 498
Author(s):  
Evolène Deslignière ◽  
Anthony Ehkirch ◽  
Bastiaan L. Duivelshof ◽  
Hanna Toftevall ◽  
Jonathan Sjögren ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Ion Mobility ◽  
State Of The Art ◽  
Native Mass Spectrometry ◽  
Site Specific ◽  
Drug Conjugates ◽  
Conjugation Process ◽  
Antibody Drug

Antibody-drug conjugates (ADCs) are biotherapeutics consisting of a tumor-targeting monoclonal antibody (mAb) linked covalently to a cytotoxic drug. Early generation ADCs were predominantly obtained through non-selective conjugation methods based on lysine and cysteine residues, resulting in heterogeneous populations with varying drug-to-antibody ratios (DAR). Site-specific conjugation is one of the current challenges in ADC development, allowing for controlled conjugation and production of homogeneous ADCs. We report here the characterization of a site-specific DAR2 ADC generated with the GlyCLICK three-step process, which involves glycan-based enzymatic remodeling and click chemistry, using state-of-the-art native mass spectrometry (nMS) methods. The conjugation process was monitored with size exclusion chromatography coupled to nMS (SEC-nMS), which offered a straightforward identification and quantification of all reaction products, providing a direct snapshot of the ADC homogeneity. Benefits of SEC-nMS were further demonstrated for forced degradation studies, for which fragments generated upon thermal stress were clearly identified, with no deconjugation of the drug linker observed for the T-GlyGLICK-DM1 ADC. Lastly, innovative ion mobility-based collision-induced unfolding (CIU) approaches were used to assess the gas-phase behavior of compounds along the conjugation process, highlighting an increased resistance of the mAb against gas-phase unfolding upon drug conjugation. Altogether, these state-of-the-art nMS methods represent innovative approaches to investigate drug loading and distribution of last generation ADCs, their evolution during the bioconjugation process and their impact on gas-phase stabilities. We envision nMS and CIU methods to improve the conformational characterization of next generation-empowered mAb-derived products such as engineered nanobodies, bispecific ADCs or immunocytokines.

Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence

2021 ◽  
Author(s):  
Lok Man ◽  
William P. Klare ◽  
Ashleigh L. Dale ◽  
Joel A. Cain ◽  
Stuart J. Cordwell
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Large Scale ◽  
Lipid A ◽  
Phenotypic Characterization ◽  
Post Translational Modification ◽  
Form Of Life ◽  
Antimicrobial Interventions

Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.

scholarly journals Potential of gas-assisted time-of-flight secondary ion mass spectrometry for improving the elemental characterization of complex metal-based systems

2020 ◽  
Vol 35 (12) ◽  
pp. 2997-3006
Author(s):  
Agnieszka Priebe ◽  
Tianle Xie ◽  
Laszlo Pethö ◽  
Johann Michler
Keyword(s):  
Mass Spectrometry ◽  
Chemical Analysis ◽  
Secondary Ion Mass Spectrometry ◽  
High Sensitivity ◽  
Elemental Distribution ◽  
Tof Sims ◽  
Molecular Information ◽  
Secondary Ion ◽  
Elemental Characterization

Enhancing the spatial resolution of TOF-SIMS, which provides 3D elemental distribution in combination with high sensitivity and molecular information, is currently one of the hottest topics in the field of chemical analysis at the nanoscale.

The growing role of structural mass spectrometry in the discovery and development of therapeutic antibodies

The Analyst ◽  
2018 ◽  
Vol 143 (11) ◽  
pp. 2459-2468 ◽  
Author(s):  
Yuwei Tian ◽  
Brandon T. Ruotolo
Keyword(s):  
Mass Spectrometry ◽  
State Of The Art ◽  
Therapeutic Antibodies ◽  
Critical Importance ◽  
Current State ◽  
Measurement Science ◽  
Structural Mass Spectrometry ◽  
Structural Mass

The comprehensive structural characterization of therapeutic antibodies is of critical importance for the successful discovery and development of such biopharmaceuticals, yet poses many challenges to modern measurement science. Here, we review the current state-of-the-art mass spectrometry technologies focusing on the characterization of antibody-based therapeutics.

Liquid chromatography mass spectrometry based characterization of epitope configurations

2020 ◽  
Vol 12 (45) ◽  
pp. 5476-5484
Author(s):  
Maren Christin Stillesby Levernæs ◽  
Arelí Urtubia Moe ◽  
Sigurd Leinæs Bøe ◽  
Elisabeth Paus ◽  
Léon Reubsaet ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Liquid Chromatography Mass Spectrometry ◽  
Three Dimensional Structure ◽  
Chromatography Mass Spectrometry ◽  
Pre Treatment

Here we evaluate a quick and easy tool for determination of epitope configuration using immunocapture and liquid chromatography mass spectrometry (LC-MS) subsequent to pre-treatment of the target protein to disrupt its three-dimensional structure.

Standardization and characterization of antigens for the diagnosis of aspergillosis

2012 ◽  
Vol 58 (4) ◽  
pp. 455-462 ◽  
Author(s):  
Cheila Denise Ottonelli Stopiglia ◽  
Alicia Arechavala ◽  
Mariana Carissimi ◽  
Julia Medeiros Sorrentino ◽  
Valério Rodrigues Aquino ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Aspergillus Niger ◽  
Sensitivity And Specificity ◽  
Predictive Value ◽  
High Sensitivity ◽  
Antigenic Activity ◽  
Sds Page ◽  
Mascot Search Engine ◽  
Commercial Kit

The aim of this study was to develop and characterize antigens for the diagnosis of aspergillosis. Nine strains of Aspergillus species Aspergillus fumigatus , Aspergillus flavus , and Aspergillus niger were grown in Sabouraud and Smith broth to produce exoantigens. The antigens were tested by immunodiffusion against sera from patients with aspergillosis and other systemic mycoses. The protein fraction of the antigens was detected by SDS–PAGE; Western blot and representative bands were assessed by mass spectrometry coupled to a nano Acquity UltraPerformance LC and analyzed by the Mascot search engine. Concurrently, all sera were tested with Platelia Aspergillus EIA. The most reactive antigens to sera from patients infected by A. fumigatus were produced by A. fumigatus MG2 Sabouraud and pooled A. fumigatus Sabouraud samples, both with a sensitivity of 93% and specificity of 100% and 97%, respectively. Aspergillus niger and A. flavus antigens were reactive against A. niger and A. flavus sera, each one with a sensitivity and specificity of 100%. Two proteins, probably responsible for antigenic activity, β-glucosidase in A. fumigatus and α-amylase in A. niger were attained. The commercial kit had a specificity of 22%, sensitivity of 100%, positive predictive value of 48%, and negative predictive value of 100%. The antigens produced showed high sensitivity and specificity and can be exploited for diagnostics of aspergilloma.

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