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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: https://www.ncqbcs.com/resources/training/summer-school

3rd Annual North American Mass Spectrometry Summer School Registration Open

Join us for our third annual mass spectrometry summer school, which will be held in Madison, WI from June 15-18. We are proud to have assembled over a dozen world leading experts in mass spectrometry for this four-day course. Our goal is to provide our students, both from academia and industry, an engaging and inspiring program covering the latest in the application of mass spectrometry to omic analyses. Tutorial lectures range from mass analyzers to the basics of data analysis. Also planned are several hands-on workshops – aimed at both scientific and professional development. This program is made possible by generous funding from the National Science Foundation (Integrated Organismal Systems, Plant Genome Research Program, Grant No. 1546742) and the National Institutes of Health National Center for Quantitative Biology of Complex Systems (P41 GM108538). As such, there is no cost to participate.

Registration open through March 1, 2020: https://www.ncqbcs.com/resources/training/summer-school.

Please help us spread the word about this program by sharing the news with anyone who might have possible interest to participate.

See below for a list of expert instructors who will be leading the courses, as well as premium tutorial lectures and hands-on workshops that you can experience.

Thank you,
Josh Coon, Evgenia Shishkova, and Laura Van Toll (organizing committee)

Expert Instructors:

Scott McLuckey | Purdue University

Rachel Loo | University of California-Los Angeles

Joshua Coon | University of Wisconsin-Madison

Donald Hunt (invited) | University of Virginia

Shawnna Buttery | STAR Protocols

Jesper Velgaard Olsen | University of Copenhagen

Lingjun Li | University of Wisconsin-Madison

Jürgen Cox | Max Planck Institute of Biochemistry

Edward Huttlin | Harvard University

Susan Olesik | Ohio State University

Evgenia Shishkova | University of Wisconsin-Madison

Jessica Prenni | Colorado State University

Vicki Wysocki | Ohio State University

John Bowden | University of Florida

Tutorial Lectures:
Mass analyzers


Tandem MS

Data acquisition


Experimental design




Top-down/Native MS


Hands-on Workshops:
Mass analyzers

Spectral interpretation
Publishing and reviewing

Science writing

Science illustrations

Software Highlight: LipiDex

LipiDex is a free and open-source software package offered by NCQBCS. This software package unifies all stages of the LC-MS/MS lipid identification process, and also utilizes intelligent data filtering to reduce manual result curation while increasing identification confidence.

One can use LipiDex to accomplish a variety of functions. For instance, one can create and manage custom in-silico lipid spectral libraries; model complex lipid MS/MS fragmentation using intuitive fragmentation templates; generate high-confidence MS/MS lipid identifications; annotate chromatographic peak tables with lipid identifications; and automatically filter peak tables for adduct peaks, in-source fragments and dimers.

Information on both LipiDex and Library Forge can be found here, and the software download is located here. Additionally, information on other software that the National Center for Quantitative Biology of Complex Systems offers can be found here.

Graphical Abstract depicting the software package lipidex accomplishing a variety of functions, such as the modeling of complex lipid ms/ms fragmentation, generation of high-confidence ms/ms lipid identifications, annotation of chromatographic peak tables, and the creation of in-silico lipid spectral libraries.

Registration for the Annual Mass Spectrometry Summer School Opens Jan 8

Registration for the 3rd annual North American Mass Spectrometry Summer School is now open.

This free event, which will take place June 15-18, 2020 in Madison, Wisconsin will feature world-leading experts in Mass Spectrometry, who will deliver lectures and tutorials on both plant (NSF) and animal (NIH) mass spec applications. 

Program details and registration can be found on the NCQBCS website, located here:

Please help us spread the word about Mass Spec Summer School by telling your colleagues and friends who might benefit from attending. 

Registration for this opportunity closes on March 1.