proteins

Viewing posts tagged proteins

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

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.

Relish protein level affects secondary traumatic brain injuries

Brain trauma is caused by both primary and secondary injuries. Primary injuries result from the physical damage to the brain, and secondary injuries from the bodies’ responses to those injuries. A recent publication in Genetics by Swanson et al. describes using mass spectrometry to investigate secondary injuries in the Relish (Rel) protein level in fly heads after a primary brain injury. They found changes in Rel levels were necessary for secondary traumatic brain injuries to occur.

Creating efficient and effective peptide fragmentation in tandem MS (MS/MS)

Photoactivation and photodissociation have long proven to be useful tools in tandem mass spectrometry, but implementation often involves cumbersome and potentially dangerous configurations. To remedy this problem, a fiber-optic cable was coupled to an infrared (IR) laser on a mass spectrometer. These advances allow for a more robust, straightforward, and safe instrumentation platform, permitting implementation of AI-ETD and IRMPD on commercial mass spectrometers and broadening the accessibility of these techniques.

This research is described in a recent Analytical Chemistry publication by Trent Peters-Clarke titled Optical Fiber-Enabled Photoactivation of Peptides and Proteins.

https://pubs.acs.org/doi/abs/10.1021/acs.analchem.0c02087

Multi-Omics of COVID-19 Collaboration with Albany Medical College

A collaboration with the lab of Dr. Ariel Jaitovich at Albany Medical College studied a Large-scale Multi-omic Analysis of COVID-19 Severity (in preprint). Over 17,000 transcripts, proteins, metabolites, and lipids were quantified and associated with clinical outcomes in a curated relational database, uniquely enabling systems analysis and cross-ome correlations to molecules and patient prognoses. A web-based tool (covid-omics.app) enables interactive exploration and illustrates its utility through a comparative analysis with published data and a machine learning prediction of COVID-19 severity.