Viewing posts from the Freebies category

MS-Helios allows 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.

Software Highlight: LipidGenie

LipidGenie is one of many free and innovative resources offered by NCQBCS.

Lipid Genie is an interactive software that can facilitate lipid identification, provide evidence for gene function, and can reveal acyl-chain specificity for ABHD1 and ABHD2.

This open-sourced software is available free and online at

Lipid Genie Logo. This logo depicts a magic lamp with a DNA helix inside, and a lipid structure exiting through the spout of the lamp.

Software Highlight: Morpheus

Morpheus, a custom search algorithm designed specifically for high-resolution tandem mass spectra, is one of many free softwares offered by NCQBCS.

Developed by the Coon Lab, Morpheus works specifically with high-mass accuracy data, and is superior to other similar programs, such as those originally designed for low-resolution MS/MS. For instance, compared to Mascot, Open Mass Spectrometry Search Algorithm (OMSSA) and Sequest, Morpheus can identify more spectra, peptides and proteins at a 1% false discovery rate. Morpheus is also 1.5-4.6 times faster than OMSSA.

Morpheus is free and open source under a permissive license.

The manuscript for Morpheus 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 for the Morpheus manual, demonstrating the algorithm's matching capabilities 
Morpheus score =10.302, 10 matching products +30.2% matching abundance.

Metandem, a free and online software for MS-based isobaric labeling metabolomics

Hao et al. (2019) recently published a paper in Analytica Chimica Acta detailing the utility of Metandem, a data analysis software which is aids in isobaric labeling-based metabolomics.

While mass spectrometry-based stable isotope labeling is advantageous compared to other methods of isotope labeling due to its multiplexing and accurate quantification capabilities, its data analysis requires specifically customized bioinformatic tools. However, Metandem, a free, unique and online software, can aid in the analysis of stable isotope labeling-based metabolomics data.

Metandem has a number of different features that assist in MS-based isobaric labeling, such as integrating feature extraction, metabolite quantification and identification, batch processing of multiple data files, online parameter optimization for custom datasets, data normalization and statistical analysis.

Metatandem is available free and online at

Graphical abstract for Metandem paper published by Hao et al in Analtica Chimica Acta demonstrating the software's utility in  isobaric labeling, integrating feature extraction, and metabolite quantification.

Registration for the 3rd Annual Mass Spec Summer School Opens in January

Registration for the NCQBCS third annual North American Mass Spectrometry Summer School will open January 2, 2020.

The NAMSS summer school is an exciting opportunity for burgeoning scientists to network and learn from leading mass spectrometry experts in both plant and animal applications.

The summer school will take place in Madison, WI from June 15-18. A variety of activities, such as lectures and workshops, will be held.

Additionally, as a summer school student, you will be able to:

Present a Poster
The poster session will be held Monday afternoon (June 15th) with prizes awarded to the top entries.

Give a Flash Talk
Flash talks will be scheduled throughout the week. They are 5-minute, one-slide presentations of your work, a research question you want input on, or something else of interest you would like to ask or share with the group. Prizes awarded to the top talks.

Future Technology Discussion
The event will include a discussion titled “Future Technology Needs”, where we want to hear your ideas of what technology is missing in the current research environment that would help advance your work. This could be techniques, protocols, instrumentation capability, etc. These can be big or small ideas, realistic or just a dream.

Join World-Leading Experts for Morning Coffee and Q&A
Sign up for a morning session where you bring your questions and get help from the experts. Sessions are limited to 15 people and we request you submit a question in advance so we can come prepared for the discussion.

Tweet Your Thoughts and Ideas
Join in via twitter during the sessions.

More information on the NAMSS 2020 summer school can be found here.

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.

2nd Summer School a Success

The 2nd Annual North American Mass Spectrometry Summer School, which took place from July 21-24 at the Wisconsin Institute for Discovery, was a success.

The event’s goal was to encourage and stimulate a community of scientists who are interested in mass spectrometry, plants and human health. This included tutorial and research lectures, workshops and a poster viewing session. Topics ranged from data analysis, chromatography and PTMs, to data integration, intellectual property and spectral interpretation, among others.

Featured speakers included Joshua Coon from the University of Wisconsin-Madison, Ulrike Kusebauch from the Institute for Systems Biology, Beatrix Ueberheide from the New York University School of Medicine, Lingjun Li from the University of Wisconsin-Madison, Judit Villen from the University of Washington, and Evan Williams from the University of California-Berkley, among many others.

Summer School was followed by the 11th Annual MaxQuant Summer School, which took place from July 24-26 in the same location. Students were able to attend one or both events.

Next year’s summer school will take place June 15-18.

For more information, visit

1st Annual North American Mass Spectrometry Summer School

Please join us for our first annual mass spectrometry summer school. 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 experimental design, sample preparation, and quantification to the basics of high performance mass analyzers and data analysis. Also planned are several hands-on workshops – aimed at both scientific and professional development. Finally, we will take a break on one afternoon for a whole group experience at nearby Devil’s Lake State Park where workshop goers can choose from a slate of exciting recreational activities. This workshop 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 and several travel awards are available.

Learn More

Register for Summer School