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02 Oct 2019

Acute-Phase proteins differ in mice with and without prostate inflammation

By nickwiecien

L. Hao et al conducted a quantitative proteomic analysis on induced prostate inflammation in mice and published a paper in the American Journal of Physiology-Renal Physiology.

Researchers compared the quantitative proteomic analysis of urine from mice with and without prostate-specific inflammation. Prostate inflammation as it is a key symptom of many different prostate conditions, such as infection and cancer, and therefore by doing so one gains a better understanding of disease mechanisms.

Researchers induced prostate-specific inflammation by conditional prostate epithelial IL-1β expression. Next, they ran urine sample tests and quantified urinary proteins. L. Hao et al found that different levels of acute-phase response proteins (proteins which have plasma concentrations that increase or decrease in response to inflammation) were represented between mice with and without prostate inflammation; these were haptoglobin, inter-α-trypsin inhibitor, and α1-antitrypsin 1-1.

Mass-spectrometry-based quantitative urinary proteomics is an important and powerful method for discovering biomarkers and uncovering molecular urological mechanisms.

Graphical abstract for Hao et al, depicting the quantitative proteomic analysis of mice urine.
25 Sep 2019

Polo-like kinase 4 maintains integrity of centriolar satellites

By nickwiecien

RA Denu et al recently published a paper on the importance of polo-like kinase 4 for centriolar satellite integrity in the Journal of Biological Chemistry.

Polo-like kinase 4 (PLK4), a Ser/Hr protein kinase, is the “master regulator” of centriole duplication and can also play a role in centrosome function. Centrioles are cell organelles which are responsible for cell division. In addition, centrioles are housed in other organelles, called centrosomes. 
This study was an attempt to identify additional proteins regulated by PLK4. To do this, scientists generated an RPE-1 human cell line and genetically engineered analog sensitive PLK4As.

Scientists found that Ser-78 is important for maintaining the integrity of centriolar satellites, as this is where PLK4 phosphorylates CEP131. Ser-78 in centrosomal protein 131 is a direct substrate of PLK4.

Another finding is that inhibiting PLK4 or using a nonphosphorylatable CEP131 tended to result in “dispersed” centriolar satellites.

18 Sep 2019

CZE and Mass Spectrometry Leads to Considerable Phosphopeptide Identification

By nickwiecien

Zhang et al demonstrated the importance and utility of Single-Shot Capillary Zone Electrophoresis in the Journal of Proteome Research.

Capillary zone electrophoresis (CZE) is a practical tool in exploring and interpreting post-translational modifications in proteins. To examine the usefulness of single-shot CZE with mass spectrometry through the analysis of phosphoproteomics, researchers used CZE separations with the Orbitrap Fusion Lumos Tribrid platform, and used a linear-polyacrylamide-coated capillary with low electroosmotic flow for separation.

Researchers found that larger injection volumes led to broader peaks and less phosphopeptide identifications. Additionally, in this single-shot phosphoproteome analysis, researchers found 4405 phosphopeptides out of an original 220 ng enriched phosphopeptides from a mouse brain.

Data for this study is available in the ProteomeXchange with identified PXD012888.

Graphical abstract for Zhang et al. This graph shows how Base Peak Intensity compares to Migration Time (in minutes). It appears that base peak intensity is higher during the 38 minute mark, the 63 minute mark, and the 65 minute mark.
11 Sep 2019

NCQBCS Scientists Publish on Essential Phosphatase Pptc7

By nickwiecien

Niemi et al analyzed a Pptc7 matrix phosphatase in mice in a recent issue of Nature Communications.

This paper addressed the functionality of phosphorylation in mitochondrial proteins. While mitochondrial proteins tend to have a lot of phosphorylation, it is also possible that protein dephosphorylation (the opposite process) may be significant in controlling various mitochondrial processes.

To test this, researchers deleted the matrix phosphatase Pptc7 from mice using the CRISPR-Cas9. As a result, mice were born with normal transcript levels but less mitochondria and protein in their tissues. They also had more phosphorylation in certain mitochondrial proteins. These mice developed hypoketonic hypoglycemia, had higher levels of acylcarnitines and serum lactate, and died shortly after being born. 

Analyzing this data, researchers pinpointed that the protein translocase complex subunit Timm50 is probably a Pptc7 substrate whose phosphorylation lowers import activity.  This data also demonstrates that Pptc7 is necessary for healthy mammalian mitochondrial processes, such as metabolism, and biogenesis after birth. 

04 Sep 2019

Brademan Paper on the Interactive Peptide Spectral Annotator

By nickwiecien

Brademan et al unveiled the Interactive Peptide Spectral Annotator (IPSA), in a recent issue of Molecular and Cellular Proteomics.

The IPSA is an interactive and easily-accessible web-based annotator that can be used to conceptualize and characterize peptides with mass spectra. This tool, which can visualize peptides collected from different experimental and instrumental sources, has a variety of purposes including creating figures for publication, annotating spectra for negative-mode ionization and the like.

The IPSA can be accessed through this link:
http://www.interactivepeptidespectralannotator.com

30 Aug 2019

2nd Summer School a Success

By nickwiecien

The 2nd Annual North American Mass Spectrometry Summer School, which took place from July 21-24 at the Wisconsin Institute for Discovery, was a success.

The event’s goal was to encourage and stimulate a community of scientists who are interested in mass spectrometry, plants and human health. This included tutorial and research lectures, workshops and a poster viewing session. Topics ranged from data analysis, chromatography and PTMs, to data integration, intellectual property and spectral interpretation, among others.

Featured speakers included Joshua Coon from the University of Wisconsin-Madison, Ulrike Kusebauch from the Institute for Systems Biology, Beatrix Ueberheide from the New York University School of Medicine, Lingjun Li from the University of Wisconsin-Madison, Judit Villen from the University of Washington, and Evan Williams from the University of California-Berkley, among many others.

Summer School was followed by the 11th Annual MaxQuant Summer School, which took place from July 24-26 in the same location. Students were able to attend one or both events.

Next year’s summer school will take place June 15-18.

For more information, visit https://www.ncqbcs.com/summer-school-2019/

11 Dec 2018

Coon Honored for Discovery in Proteomic Sciences

By nickwiecien

Joshua Coon, PhD, professor of biomolecular chemistry and chemistry has been awarded a Discovery in Proteomic Sciences Award from the Human Proteome Organization (HUPO).

HUPO is an international organization that represents and promotes proteomics through global cooperation and collaborations by fostering the development of new technologies, techniques and training.The award recognizes Prof. Coon’s outstanding effort and achievement in proteomics, the study of cellular proteins and their functions.

The Coon lab team develops and applies mass spectrometric technology to study human health and develop scientific instruments to measure molecules in living systems. Prof Coon has made significant contributions to proteomics and metabolomics research by developing next-generation instrumentation and methods, proteomics workflows, novel isotopic labeling quantitative approaches and associated software development. Coon’s work has influenced many labs in the United States and abroad, and the tools he has created are in use throughout the world.

Coon is the inaugural holder of the Thomas and Margaret Pyle Chair at UW-Madison and an affiliate of the Morgridge Institute for Research. He presently serves as director of the National Institute of General Medical Science funded National Center for Quantitative Biology of Complex Systems. He joined the UW-Madison faculty in 2005.

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