Publications

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Fast, unbiased proteome quantification without LC

Liquid chromatography–mass spectrometry (LC–MS) delivers sensitive peptide analysis for proteomics but requires extensive analysis time, reducing productivity. A recent paper by Meyer et al. titled “Quantitative shotgun proteome analysis by direct infusion” demonstrated that gas-phase peptide separation using direct infusion–shotgun proteome analysis enabled fast, unbiased proteome quantification without LC, and offered an approach to boost throughput, critical to studies that require analysis of thousands of proteomes.

Gut microbiome may play a role in brain functions and behaviors

Gut microbiota can regulate host physiological and pathological status through gut–brain communications or pathways. However, the impact of the gut microbiome on the proteins involved in regulating brain functions and behaviors is still not clearly understood. In a recent publication by Liu et al., the author describes a combined label-free and 10-plex DiLeu-based quantitative method that enabled a comprehensive profiling of gut microbiome that induced dynamic changes, suggesting that the gut microbiome might mediate a range of behavioral changes, brain development, and learning and memory through these neuropeptides and proteins.

Liu R et al. Integrated Label-Free and 10-plex DiLeu Isobaric Tag Quantitative Methods for Profiling Changes in the Mouse Hypothalamic Neuropeptidome and Proteome: Assessment of the Impact of the Gut Microbiome. Analytical Chemistry.

Argonaut enables collaborative data visualization and exploration

Argonaut is an online platform for collaborative exploration of multi-omic data described in this recent publication by Brademan et al.

Through this platform, information is presented using intuitive, interactive visualizations in a code-free environment, empowering both experts and non-experts worldwide to easily interact and share data.

The Argonaut platform aims to overcome the hurdles of working with large datasets and lower the barrier to entry for biological and clinical collaborators.

This and other software tools can be found here.

DiLeu tagging for protein and phosphorylation quantification in parallel

For the first time, DiLeu tagging has been implemented for protein and phosphorylation quantification in parallel. This process was described in a recent publication by Zhong et al titled Highly multiplexed quantitative proteomic and phosphoproteomic analyses in vascular smooth muscle cell dedifferentiation.

The research team developed a strategy that used 12-plex N,N-dimethyl leucine (DiLeu) isobaric tags together with the DiLeu software tool to globally assess protein expression and phosphorylation changes in smooth muscle cells (SMCs) treated with TGFβ/Smad3 and/or SDF-1α (stromal cell-derived factor).

The goal of this work was to develop insights into the mechanisms of TGFβ regulated SMC dedifferentiation, as well as effective therapeutics for vascular disease.

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

Training opportunity leads to publication

In early 2020, a group of researchers from the University of Copenhagen spent a week at NCQBCS facilities to learning more about Activated Ion Electron Transfer Dissociation (AI-ETD) and how to apply it to their research. That training has led to a publication in Cell Reports titled Mapping physiological ADP-ribosylation using Activated Ion Electron Transfer Dissociation (AI-ETD). This work describes the use of AI-ETD for mass spec-based proteomics analysis of ADPr, which is known to play a pivotal role in a wide range of cellular processes.

For more information on training opportunities offered by NCQBCS visit the training section of our website.

Li lab project uses DiLeu isobaric labeling to monitor neurotoxicity in chemotherapy in children

A new project by the Lingjun Li lab explores the use of the 4-plex N,N-dimethyl leucine (DiLeu) isobaric labeling strategy for protein identification and quantification in cerebrospinal fluid in children undergoing chemotherapy. The results from this and future studies will provide a means to monitor neurotoxicity and develop strategies to prevent central nervous system injury in response to chemotherapy in children.

The publication is Isobaric labeling strategy utilizing 4-plex N,N-dimethyl leucine (DiLeu) tags reveals proteomic changes induced by chemotherapy in cerebrospinal fluid of children with B-cell acute lymphoblastic leukemia from the Journal of Proteome Research.

New publication looks at the biomarkers of COPD in skeletal muscle integrity response to exercise

A collaboration between the Coon group and the lab of Ariel Jaitovich at Albany Medical College looked at patients with chronic Pulmonary disease (COPD) who developed muscle dysfunction, a condition associated with higher mortality rates and poor outcomes for these individuals. This study was a large-scale analysis of the mouse muscle proteome to identify the significant upregulated proteins contributing to muscle dysfunction.

Read the full article, Established biomarkers of COPD reflect skeletal muscle integrity’s response to exercise in an animal model of pulmonary emphysema, by Balnis et al.

Li lab identifies metabolite and protein biomarkers to identify prostatic inflammation with lower urinary tract symptoms

Lower urinary tract symptoms (LUTS) are common among aging men. Since inflammation is one of its indicators, it is plausible that urinary metabolite and protein biomarkers could be used to identified and diagnose inflammation-induced LUTS. In this study, the Li lab used Mass spectrometry (MS)-based multi-omics analysis to characterize the urine metabolome and proteome in a mouse model. By comparing their findings with urinary biomarkers associated with LUTS in older men, they identified creatine, haptoglobin, immunoglobulin kappa constant and polymeric Ig receptor as conserved biomarkers for prostatic inflammation associated with LUTS.

The full article, Urinary metabolomic and proteomic analyses in a mouse model of prostatic inflammation, can be viewed here.

DiLeu isobaric tags achieves 21-plex quantification

Isobaric tags enable multiplexed quantitative analysis of many biological samples in a single LC-MS/MS experiment. As a cost-effective alternative to expensive commercial isobaric tagging reagents, the lab of Lingjun Li has developed their own custom “DiLeu” isobaric tags for quantitative proteomics. In this paper, Dustin Frost showcases a new generation of DiLeu tags that achieves 21-plex quantification in high-resolution HCD MS/MS spectra.

21-plex DiLeu Isobaric Tags for High-throughput Quantitative Proteomics. Analytical Chemistry.