Mass Spectrometry

Viewing posts tagged Mass Spectrometry

COVID-19: A lesson in community working for the public good

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

Recent publication highlights phosphoproteome analysis using FAIMS

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

Li lab identifies metabolite and protein biomarkers to identify prostatic inflammation with lower urinary tract symptoms

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.

The full article, Urinary metabolomic and proteomic analyses in a mouse model of prostatic inflammation, can be viewed here.

DiLeu isobaric tags achieves 21-plex quantification

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 for Compact Data Visualization of Multi-omic Datasets

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.

Summer School Registration Closes Soon

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:

Software Highlight: Compass

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.

NCQBCS Offers Broad Range of Training Programs for all Levels of Learners

A key goal of the National Center for Quantitative Biology of Complex Systems is to extend its expertise to the broader scientific community. Therefore, NCQBCS offers hands-on-training programs ranging from basic basic proteomic methodology to advanced technological techniques.

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.

Increasing MS lipidomics power through parameter optimization and In Silico Simulation

Hutchins et al (2019) recently published a paper in Analytical Chemistry presenting an algorithm which identifies parameter sets in a way that is quicker and more accurate than typical methods.

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.

Graphical abstract from Hutchins et al (2019) which details the parameter optimization and in silico simulation methods.
Instrument parameters --> model MS acquisition --> simulate lipid IDs.

Fixed mass-to-charge ratio scan ranges generates more MS/MS scans than standard approaches

Trujillo et al (2019) published an article on maximizing tandem mass spectrometry acquisition rates for shotgun proteomics in a recent issue of Analytical Chemistry.

While advances in mass spectrometry (MS/MS) have lead to increased performance in shotgun proteomics experiments, ion trap scan duration is highly variable and often depends on the mass of the precursor.

Looking into this variability, the authors compared the performance of various static mass-to-charge ratio scan ranges for ion trap MS/MS acquisition to conventional dynamic mass-to-charge ratio scan ranges. Compared to the standard dynamic approach, the fixed mass-to-charge ratio scan range generated 12% more MS/MS scans and identified more unique peptides.

Graphical abstract for Trujillo et al (2019) depicting a graph titled "Increase # MS/MS collected." We see that as the maximum ion injection time decreases, the number of MS/MS collected increases. Additionally, as the m/z scan range increases, the # of MS/MS increases as well.