This paper by Sauer et. al. is focused on developments in mass spectrometry for labeling strategies, post-translational modification analysis, mass spectrometry imaging, and integrated multi-omic workflows, with discussion emphasizing quantitative advancements.
Read the article: Developing mass spectrometry for the quantitative analysis of neuropeptides.
In a new longform story, the Morgride Institute of Research scientists and researchers reflect on what collectively happened in late 2019, as the novel coronavirus began spreading and along with it deep uncertainty and unprecedented challenges.
This is a science and also a story about how people and communities came together to work for the public good. It is about the lessons learned and those that still remain. It features the experiences of researchers Tim Grant, Josh Coon, Tony Gitter, Melissa Skala, and Paul Alhquist, and many others.
Read about it here: Resilience: How COVID-19 challenged the scientific world
Mass spectrometry is the premier tool for identifying and quantifying protein phosphorylation. Analysis of phosphopeptides requires enrichment, and even after that step, the samples remain highly complex and exhibit broad dynamic range of abundance. In a recent publication, Muehlbauer et al. describe a method for integrating a high-field asymmetric waveform ion mobility spectrometry (FAIMS) device into the workflow. The data collected with FAIMS yielded a 26% increase in total reproducible measurements, leading researchers to conclude that the new FAIMS technology is a valuable addition to any phosphoproteomic workflow, with greater benefits emerging from longer analyses and higher amounts of material.
Read the publication here: Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer
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.
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.
MS-Helios is an easy-to-use command line tool which works to solve the challenge of data analysis and visualization in the face of high-resolution mass spectrometery.
Though high-resolution mass spectrometry can identify hundreds of metabolites and thousands of proteins, this can make data analysis and visualization hard to do.
MS-Helios is a solution, allowing for compact data representation and reduced dimensionality. This tool also allows non-experts and experts alike to generate data and configuration files and publish high-quality, circular plots with Circos.
This software is available for download here.
The manuscript for MS-Helios can be viewed here.
Registration for the 3rd Annual North American Mass Spectrometry Summer School will close on March 1.
This means time is running out to sign up for 4 free days of learning, tutorial lectures, and hands-on-workshops– all led by world-leading experts in mass spectrometry.
The goal of this event– which will take place from June 15-18 at the Wisconsin Institute for Discovery– is to provide an engaging and inspiring program to students by combining networking, education and discovery and housing it all under one roof.
Specifically, this program covers the latest in application of mass spectrometry to omic analyses, from both industry and academic lenses. With tutorial lectures covering a variety of topics, from mass analyzers to lipidomics, and hands-on-workshops aimed at both scientific and professional development, this program is not one you would want to miss. Don’t forget to tell your peers about this excellent opportunity!
Registration is available at the following link: https://www.ncqbcs.com/resources/training/summer-school
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.
NCQBCS, which works to develop next-generation protein measurement technologies for biomedical application, has programs available for a wide range of students. This means that there are introductory training programs available for those interested in learning the basics of mass spectrometry, as well as programs geared for experts on specific technologies.
NCQBCS divides its training topics into four broad categories: Sample Preparation, Instrumentation, Data Analysis, and Protein Quantification. Trainees can build their own syllabus of workshops from a variety of categories and experience levels.
Comprehensively, we offer programs in:
Sample Preparation: Peptide Fractionation, Protein Digestion, Protein extraction.
Mass Spectrometry: MS Methods, Instrument Troubleshooting, Nano-chromatography.
Data Analysis: Data Visualization, Data Interpretation, Data Searching.
Protein Quantification: Label-free, Metabolic labeling, Isobaric chemical labeling.
More information on our training programs are located here, and one can sign up for training here.
Additionally, one can also receive coaching at the 3rd Annual North American Mass Spectrometry Summer School, which will take place June 15-18, 2020. This event, which will be hosted by international experts on Mass Spectrometry, will feature workshops, lectures and networking, among other activities.
One may find more information, as well as sign up for summer school, here.
The issue of effectively profiling the diversity and range of biomolecules is an important one to consider in Mass Spectrometry, and relies on well-sought out selection of acquisition parameters. However, acquisition parameters are generally selected in a way that is time-consuming and tends to produce lacking results.
By creating an algorithm which simulates LC-MS/MS lipidomic data acquisition performance in a benchtop quadrupole-Orbitrap Mass Spectrometer system and pairing it with an algorithm that defines constrained parameter optimization, researchers were able to efficiently identify LC-MS/MS method parameter sets for specific sample matrices. Additionally, researchers used a simulation called in silico to demonstrate how developments in mass spectrometer speed and sensitivity will result in even more effective biomolecule identification.
