This paper by Sauer et. al. is focused on developments in mass spectrometry for labeling strategies, post-translational modification analysis, mass spectrometry imaging, and integrated multi-omic workflows, with discussion emphasizing quantitative advancements.
Read the article: Developing mass spectrometry for the quantitative analysis of neuropeptides.
Beyond its role in mitochondrial bioenergetics, Coenzyme Q (CoQ, ubiquinone) serves as a key membrane-embedded antioxidant throughout the cell. However, how CoQ is moved from its site of synthesis on the inner mitochondrial membrane to other sites remains a longstanding mystery. In a recent study, researchers identified two highly conserved but poorly characterized mitochondrial proteins that affect this process. Their results reveal the protein machinery central to CoQ trafficking in yeast and lend insights into the broader interplay between mitochondria and the rest of the cell.
Read the article: UbiB proteins regulate cellular CoQ distribution in Saccharomyces cerevisiae
Evgenia Shishkova has developed a new protocol that offers step-by-step instructions for preparation of raw blood plasma for liquid chromatography – tandem mass spectrometry (LC-MS/MS). The technique is simple, robust, and reproducible. The entire transformation only takes 3–4 h. This protocol can be adopted for large-scale studies and automation.
Process is available in STAR Protocols: Rapid preparation of human blood plasma for bottom-up proteomics analysis
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
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.
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.
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.
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
Despite the crucial roles of lipids in metabolism, we are still in the early stages of annotating lipid species and their genetic basis. To help in this work, a team of researchers led by Vanessa Linke recently developed LipidGenie, an interactive, query-able resource for lipid identification. The research team used high-resolution liquid chromatography–tandem mass spectrometry to quantify 3,283 molecular features from the liver and plasma of outbred mice. These features were then mapped to 5,622 lipid quantitative trait loci, compiled and cross-referenced to the human genome.
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.
