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CZE and Mass Spectrometry Leads to Considerable Phosphopeptide Identification

Zhang et al demonstrated the importance and utility of Single-Shot Capillary Zone Electrophoresis in the Journal of Proteome Research. Authors include members of the Coon Lab: AS. Hebert, MS. Westphall and JJ. Coon.

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.

NCQBCS Scientists Publish on Essential Phosphatase Pptc7

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. 

Brademan Paper on the Interactive Peptide Spectral Annotator

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:

2nd Summer School a Success

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

McKetney Publishes “Proteomic Atlas of the Human Brain in Alzheimer’s Disease”

Justin McKetney et. al. recently published a paper on neurodegenerative diseases of the brain, such as Alzheimer’s disease (AD). Using state-of-the-art mass spectrometry, the group identified a core brain proteome where substantial differences were identified between previous proteomic studies of mature adult brains and their aged cohort. These findings suggest considerable value in examining specifically the brain proteome of aged human populations and can serve as a guide for how specific regions of the brain are affected by aging and neurodegeneration.

Article selected for Journal of Biological Chemistry 2018 Collection

The Mitok/Coon/Attie article “Islet proteomics reveals genetic variation in dopamine production resulting in altered insulin secretion” was selected as the representative ‘Genomics and proteomics’ article for the Journal of Biological Chemistry 2018 Retrospective Collection called “The year in JBC: 2018.” When choosing the representative articles, the journal editors considered hundreds of papers to come up with what they felt best represented the exciting advances reported in JBC last year. This special issue can be found at

Coon Honored for Discovery in Proteomic Sciences

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.

Dr. Shishkova’s article chosen by Springer Nature’s Change the World initiative for 2018

Dr. Shishkova’s article, titled “Gender Diversity in a STEM Subfield – Analyses of a Large Scientific Society and Its Annual Conferences,” was recently chosen by Springer Nature’s Change the World initiative for 2018. The article can be found listed under the ” Chemistry, Engineering, Physics & Materials” category.

The Change the World, One Article at a Time initiative selects scientific findings published in 2017 that can have an impact on society’s most pressing problems. Congratulations to Dr. Shishkova for this recognition!

Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys

Caloric restriction extends lifespan and delays aging in diverse species. On pp. 677–688 of the current issue of Cell Metabolism, Rhoads et al. integrated large-scale data from the hepatic transcriptome, proteome, and metabolome of rhesus monkeys after 2 years on a 30% calorie-restricted diet to reveal multi-modal mechanisms driven by calorie restriction to rewire metabolism. The panels of the cover image represent the four distinct regulatory strategies recruited by caloric restriction: transcriptional, post-transcriptional, translational, and post-translational, each of which gives a different “view” of the unified and integrated molecular response to caloric restriction.