proteomics

Viewing posts tagged proteomics

11 Jun 2020

Recent research shows activated ion electron transfer dissociation has better performance for proteoform fragmentation

By nickwiecien

Elijah McCool, a graduate student in Lab of Dr. Liangliang Sun at Michigan State University, recently published on a collaboration with NCBBCS, Capillary Zone Electrophoresis-Tandem Mass Spectrometry with Activated Ion Electron Transfer Dissociation for Large-scale Top-down Proteomics. in the Journal of The American Society for Mass Spectrometry.

Capillary zone electrophoresis-tandem mass spectrometry is recognized as an efficient approach for top-down proteomics because of its high-capacity separation and highly sensitive detection of proteoforms. However, the commonly used collision-based methods often don’t provide the extensive fragmentation needed for thorough characterization of proteoforms. Activated ion electron transfer dissociation (AI-ETD), which combines infrared photoactivation with ETD, has shown better performance for proteoform fragmentation than other methods.

03 Jun 2020

Collaboration Yields Insight on Role of Metabolism in Bacterial Growth

By nickwiecien

Bacterial biofilms are everywhere in nature and play an important role in many clinical, industrial, and ecological settings. Although much is known about the transcriptional regulatory networks that control biofilm formation in model bacteria such as Bacillus subtilis, very little is known about the role of metabolism in this process. To address this important knowledge gap, this study used a time-resolved analysis of the metabolic changes associated with bacterial biofilm development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. This report serves as a unique resource for future studies and will be relevant to future research in microbial physiology and metabolism. The full publication can be found here.

06 Feb 2020

A Strategy for Increasing Analytical Throughput in Quantitative Proteomics

By nickwiecien

Zhong et al (2019) developed a novel strategy aimed towards solving challenges in absolute quantification, and detailed these efforts in a recent issue of Analytical Chemistry.

Absolute quantification is both an effective technique– which allows for robust results in proteomics research– and a challenging one. Problems that absolute quantification presents include low specificity in complex backgrounds, limited analytical throughput and wide dynamic range.

To solve these issues, Zhong et al (2019) developed hybrid offset-triggered multiplex absolute quantification (HOTMAQ), a strategy which increases the analytical throughput (the increase in analysis production rate) of targeted quantitative proteomics by up to 12 times. This technique accomplishes this by using mass-difference and isobaric tags to create an internal standard curve in the MS1 precursor scan, identify peptides at the MS2 level, and mass offset-trigger the quantification of target proteins in synchronous precursor selection at the MS3 level. All of this is accomplished at the same time. 

Because HOTMAQ results in greater quantitative performance, higher flexibility and quicker analysis rate, HOTMAQ is a strategy that can easily be applied to target peptidomics, proteomics, and phosphoproteomics.

Graphical Abstract, demonstrating the technique of hybrid offset-triggered multiplex absolute quantification (HOTMAQ). "Zhong, X., Q. Yu, F. Ma, D.C. Frost, L. Lu, Z. Chen, H. Zetterberg, C. Carlsson, O. Okonkwo, and L. Li, Hotmaq: A multiplexed absolute quantification method for targeted proteomics. Analytical Chemistry, 2019. 91(3): p. 2112-2119. PMCID: PMC6379083"
27 Nov 2019

Software Highlight: Compass

By nickwiecien

The Coon OMSSA Proteomic Analysis Software Suite, or COMPASS, is one of many custom software and web-based data tools that NCQBCS offers in an effort to extend its expertise to the broader scientific community.

Compass is a free and open-source software pipeline designed around the Open Mass Spectrometry Search Algorithm. Compass aids in high-throughput analysis of proteomics data such as FASTA database creation, peptide-spectral matching, calculation of false discovery rates, and protein grouping, as well as spectral reduction, peptide quantitation via isobaric labeling (or without), and protein parsimony.

Furthermore Compass utilizes graphical user interfaces which work well with data files in original instrument vendor format, making it easy to use.

The manuscript for Compass is available here, and the software can be downloaded here. Additionally, information on other software that the National Center for Quantitative Biology of Complex Systems offers can be found here.

Graphical abstract from the COMPASS manual, demonstrating its uses as a database maker, dta generator, fdr optimizer, and protein herder.
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