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COVID-19: A lesson in community working for the public good

In a new longform story, the Morgride Institute of Research scientists and researchers reflect on what collectively happened in late 2019, as the novel coronavirus began spreading and along with it deep uncertainty and unprecedented challenges.

This is a science and also a story about how people and communities came together to work for the public good. It is about the lessons learned and those that still remain. It features the experiences of researchers Tim Grant, Josh Coon, Tony Gitter, Melissa Skala, and Paul Alhquist, and many others.

Read about it here: Resilience: How COVID-19 challenged the scientific world

New features in Coenzyme Q identitifed

Coenzyme Q (CoQ), an essential lipid, is manufactured by virtually all cells, but how eukaryotes make the universal CoQ head group precursor 4-hydroxybenzoate (4-HB) from tyrosine is unknown. In this study, Robinson et al. study this pathway with genetic screens, targeted LC-MS, and chemical genetics. The results of their work defines new features of 4-HB synthesis in yeast, demonstrate the redundant nature of this pathway, and provide a foundation for further study.

Read the article: Defining intermediates and redundancies in coenzyme Q precursor biosynthesis

Introducing DiLeuPMP, a multiplexed isobaric labeling method

Glycosylation plays an important role in how the human body functions, including cell recognition, signaling, and immune response. While efforts have been devoted to the analysis of N-glycans, high-throughput quantitative analysis of O-glycans is underexplored. In this study, a multiplexed isobaric labeling method, DiLeuPMP, is introduced. This method combines the release and labeling of O-glycans in one step and achieves accurate MS2-based relative quantification. This method provides an effective and reliable approach for the profiling and high-throughput quantitative analysis of O-glycans in complex samples.

Read the article: DiLeuPMP: a multiplexed isobaric labeling method for quantitative analysis of O-glycans

The science behind how soy sauce tastes

Soy sauce is a naturally fermented global condiment. It is complex in its chemical profile of salts and organic compounds, but is susceptible to deterioration after bottling. This study by Reddy et al. examined soy sauces over an eight-month period using sensory testing, such as taste and smell, and identifying metabolomic biomarkers using mass spectrometry. They found that changes in soy sauce resulting from storage have decreases in fruity/grape and nutty/sesame taste and aroma, increases in methional/potato aroma and astringent attributes. These taste and smell differences were confirmed with mass spectrometry, which identified changes in the concentrations of several key biomarkers.

Read the article: Metabolomic Biomarkers Differentiate Soy Sauce Freshness under Conditions of Accelerated Storage

Data suggest a unique inflammatory signature associated with severe COVID19

The COVID19 pandemic will cause more than a million of deaths worldwide, primarily due to complications from acute respiratory distress syndrome (ARDS). Controversy surrounds the current cytokine/chemokine profile of COVID19-associated ARDS, with some groups suggesting that it is similar to non-COVID19 ARDS patients and others observing substantial differences. Balnis et. al. conducted a study of 41 mechanically ventilated patients with COVID19 infection using highly calibrated methods to define the levels of plasma cytokines/chemokines. Plasma IL1RA and IL8 were found positively associated with mortality, while RANTES and EGF negatively associated with that outcome. However, the leukocyte gene expression of these proteins had no significant correlation with mortality. Their data suggest a unique inflammatory signature associated with severe COVID19.

Read the article: Unique inflammatory profile is associated with higher SARS-CoV-2 acute respiratory distress syndrome (ARDS) mortality

Chemical labeling for glycan and glycopeptide quantitation

Growing implications of glycosylation in human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by an increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. In this review, Delafield and Li present the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification.

Read the article: Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation

Biologically relevant proteins in Alzheimer’s Disease

Proteomic analysis of cerebrospinal fluid (CSF) holds great promise in understanding the progression of neurodegenerative diseases, including Alzheimer’s disease (AD). As one of the primary reservoirs of neuronal biomolecules, CSF provides a window into the biochemical and cellular aspects of the neurological environment. Using mass spectrometry technologies, McKetney et. al. quantified 700 proteins across 10 pairs of age- and sex-matched participants. Using the paired structure, they identified a small group of biologically relevant proteins that show substantial changes in abundance between normal and AD participants. These findings suggest the utility of fractionating a single sample and using matching to increase proteomic depth in CSF.

Read the article: Pilot Proteomic Analysis of Cerebrospinal Fluid in Alzheimer’s Disease. Proteomics Clinical Applications.

Achieving a simplified, multi-omics workflow

An article by Yuchen He et. al. titled “Multi-omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis” was recently published as one of the cover stories in Analytical Chemistry.

This article describes a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through Multi-omics (proteome, lipidome, and metabolome) single-shot technology (MOST), requiring only one column, one LC-MS instrument, and a simplified workflow.

Adding FAIMS to the phosphoproteomic workflow

Mass spectrometry is the premier tool for identifying and quantifying protein phosphorylation on a global scale. Analysis of phosphopeptides requires enrichment, and even after the samples remain highly complex and exhibit a broad dynamic range of abundance. A recent publication by Muehlbauer et. al. found that incorporating a commercialized aerodynamic high-field asymmetric waveform ion mobility spectrometry (FAIMS) device into the phosphoproteomic workflow was a valuable addition with greater benefits emerging from longer analyses and higher amounts of material.

Read the article, Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer.

Recent publication highlights phosphoproteome analysis using FAIMS

Mass spectrometry is the premier tool for identifying and quantifying protein phosphorylation. Analysis of phosphopeptides requires enrichment, and even after that step, the samples remain highly complex and exhibit broad dynamic range of abundance. In a recent publication, Muehlbauer et al. describe a method for integrating a high-field asymmetric waveform ion mobility spectrometry (FAIMS) device into the workflow. The data collected with FAIMS yielded a 26% increase in total reproducible measurements, leading researchers to conclude that the new FAIMS technology is a valuable addition to any phosphoproteomic workflow, with greater benefits emerging from longer analyses and higher amounts of material.

Read the publication here: Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer