Uncategorized

Viewing posts from the Uncategorized category

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:
http://www.interactivepeptidespectralannotator.com

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.