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Software Hero



Continued improvements in mass spectrometry technology and throughput have empowered our lab to tackle increasingly larger and more complex biological problems. As the MS datasets we generate expand in size, we have started to explore improved mediums for analyzing and disseminating data with collaborators and biochemical researchers worldwide.

list of Software

Our Tools

Check out our custom software and web-based data tools



Argonaut is a simple, code-free, and user-friendly platform for creation of interactive data-hosting websites. Argonaut conducts real-time statistical analysis of measured bio molecules,visualizes data using popular plots, and can be securely shared with and explored by collaborators across the globe

Manuscript   Get the Software



A free and open-source software package which unifies all stages of LC-MS/MS lipid identification, empowering intelligent data filtering to greatly reduce manual result curation and increase identification confidence.

Manuscript LipiDex Library Forge Get the Software


Interactive Peptide Spectral Annotator (IPSA)

A web-based utility for the annotation of shotgun proteomics mass spectrometry data. IPSA generates interactive visualizations from bottom-up proteomic workflows. These visualizations can be exported in SVG format and annotated fragment ions and additional metrics can be exported in CSV format.

manuscript Get the Software


An easy to use command line tool with multiple built-in data processing functions, allowing non-expert users to construct circular proteome maps. MS-Helios automatically generates data and configuration files to create high quality and publishable circular plots with Circos.

Manuscript Get the Software


An interactive, query-able resource to facilitate lipid identification, provide evidence for gene function, and when queried for either lipid ID or gene ID, reveal acyl-chain specificity for ABHD1 and ABHD2, respectively.

Manuscript Get the Software

COVID-19 Multi-Omics Dashboard

A web-based tool enabling interactive exploration of published data and a machine learning approach for prediction of COVID-19 severity.

Manuscript Get the Software


A free data analysis platform for mass spectrometry-based isobaric labeling metabolomics. It allows users to upload and process MS or hyphenated MS data files for isobaric-labeling-based quantitative and qualitative metabolomics analyses, including feature extraction, metabolite quantification, metabolite identification, batch processing of multiple data files, parameter optimization, median normalization, and statistical analysis. Results can be downloaded or visualized online.

Manuscript Get the Software


A free and open-source software pipeline for high-throughput analysis of proteomics data, designed around the Open Mass Spectrometry Search Algorithm. COMPASS supports all functions required for searching proteomics data including: FASTA database creation, peptide-spectral matching, calculation of false discovery rates, and protein grouping.

manuscript Get the Software


A custom search algorithm developed by the Coon Research lab designed from the ground up for high-resolution tandem mass spectra. We have discovered that for high-resolution MS/MS, simple spectrum preprocessing and scoring performs superior to more complex algorithms originally developed for low-resolution MS/MS, such as Sequest, Mascot, and OMSSA. 

manuscript Get the Software

High-Resolution Filtering

An algorithm designed to exploit the high-resolution measurements afforded by the Thermo Fisher Q-Exactive GC mass spectrometer platform to improve identification of profiled metabolites and other small molecules.


Web-based data sharing

We have built custom online data exploration tools in support of numerous projects and are actively developing new tools to enable MS researchers worldwide to share and explore data directly from a web browser.

The Y3K project Medicago




Software We Love

Check out some of our favorites



An all-encompassing data processing software suite for proteomic data. MaxQuant handles everything from database searching to quantitation.

manuscript         Get the Software


A post-data-processing software tool for rapid visualization and statistical analysis of “omics” data. \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\

manuscript        Get the Software



An open-source peptide-spectral matching algorithm designed for bottom-up proteomic data. OMSSA has been a staple in our day-to-day data processing routine for years.

manuscript        Get the Software

ProSight PMT 2.0

A search algorithm designed to identify proteins surveyed using a top-down approach.    \\\ \\\\\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\

manuscript        Get the Software



A freely available code library for generating interactive visualizations and plots in a web-based environment. D3 makes data exploration easy and fun.

manuscript        Get the Software


A web-based tool we routinely use to find gene ontology (GO) term enrichments in biological MS data. \\\\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\   

manuscript        Get the Software



For additional information about NCQBCS please send your contact details using the form below.
Note, if you are interested in training, please use the form on our training page.


For additional information about NCQBCS please send your contact details (name, institution, email) along with a short description of how we can help to laura[dot]vantoll[at]wisc[dot]edu.

Note, if you are interested in training, please use the form on our training page.

Coon Lab, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI
Li Lab, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI
Pagliarini Lab, Washington University School of Medicine, 4523 Clayton Ave, St. Louis, MO