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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.

07 Oct 2020

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

By nickwiecien

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.

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.

22 Jul 2020

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

By nickwiecien

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.

15 Jul 2020

Collaboration yields insights into iron restriction for limiting pathogen growth

By nickwiecien

A recent collaboration titled Tailoring a Global Iron Regulon to a Uropathogen looks at host iron restriction as a mechanism for limiting the growth of pathogens. The study compared the regulatory network controlled by Fur in uropathogenic E. coli (UPEC) to that of nonpathogenic E. coli K-12 to uncover strategies that bacteria use to overcome iron limitation. Although iron homeostasis functions were regulated by Fur in the uropathogen as expected, a surprising finding was the activation of the stringent and general stress responses in the uropathogen fur mutant, which was rescued by amino acid addition. This coordinated global response could be important during transitions from the nutrient-rich environment of the lower gastrointestinal tract to the more restrictive environment of the urinary tract.

08 Jul 2020

Collaboration explores the role of N-glycans during vertebrate development

By nickwiecien

A collaboration with the lab of Norman Dovichi at the University of Notre Dame explores the role of N-glycans in biological processes during vertebrate development. In a recent publication, Quantitative Capillary Zone Electrophoresis-Mass Spectrometry Reveals the N-glycome Developmental Plan during Vertebrate Embryogenesis, they report on the first quantitative studies of both the expression of N-linked glycans at six early development stages and the expression of N-glycosylated peptides at two early development stages in the African clawed frog. In the study, N-Glycans were labeled with isobaric tandem mass tags and characterized using tandem mass spectrometry. Over two thirds of the N-glycoproteins identified in the late stage were associated with neuron projection morphogenesis, suggesting a vital role of the N-glycome in neuronal development.

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