proteomics

Viewing posts tagged proteomics

08 Dec 2020

Fast, unbiased proteome quantification without LC

By nickwiecien

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.

02 Dec 2020

Gut microbiome may play a role in brain functions and behaviors

By nickwiecien

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.

04 Nov 2020

DiLeu tagging for protein and phosphorylation quantification in parallel

By nickwiecien

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.

15 Oct 2020

Training opportunity leads to publication

By nickwiecien

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.

24 Sep 2020

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

By nickwiecien

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.

02 Sep 2020

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

By nickwiecien

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.

19 Aug 2020

DiLeu isobaric tags achieves 21-plex quantification

By nickwiecien

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.

05 Aug 2020

Li lab collaboration yields insights into spinal cord stimulation for pain relief

By nickwiecien

A recent publication by Tilley et al titled Proteomic modulation in the dorsal spinal cord following spinal cord stimulation therapy in an in vivo neuropathic pain model, explores how Spinal cord stimulation (SCS) can provide relief for patients suffering from chronic pain, with less dependence on electrical interference. Recent evidence has been growing regarding molecular changes that are induced by SCS as being a key player in reversing the pain process. In this paper the effect of SCS on altering protein expression in spinal cord tissue using a proteomic analysis approach are observed.

01 Jul 2020

Li lab collaboration explores noninvasive markers in prostate disease diagnosis

By nickwiecien

A recent collaboration between the labs of Lingjun Li and William Ricke explores the relationship between prostatic hyperplasia and related lower urinary tract symptoms in aging males and how noninvasive markers could be helpful in disease diagnosis. This proteomics study used a mouse model of hormone-induced urinary dysfunction to gain insight into the disease and supports the concept of noninvasive urinary biomarkers being a successful route for prostate disease diagnostics.

Thomas S, Hao L, DeLaney K, McLean D, Steinke L, Marker PC, Vezina CM, Li L, Ricke WA. Spatiotemporal proteomics reveals the molecular consequences of hormone treatment in a mouse model of lower urinary tract dysfunction. Journal of Proteome Research. 2020, 19(4):1375-1382.

17 Jun 2020

Collaboration with Puglielli lab reveals AT-1 acts as metabolic regulator for acetyl-CoA

By nickwiecien

In a paper titled Acetyl-CoA Flux Regulates the Proteome and Acetyl-Proteome to Maintain Intracellular Metabolic Crosstalk, Inca Dieterich et al. of Prof Luigi Puglielli’s lab investigated two models of AT-1 dysregulation and altered acetyl-CoA flux: AT-1S113R/+ mice, a model of AT-1 haploin sufficiency, and AT-1 sTg mice, a model of AT-1 overexpression. The animals display distinct metabolic adaptation across intracellular compartments, including reprogramming of lipid metabolism and mitochondria bioenergetics. Our results suggest that AT-1 acts as an important metabolic regulator that maintains acetyl-CoA homeostasis by promoting functional crosstalk between different intracellular organelles.

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