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Software Hero

 

Software

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. Check out some of these tools below!

list of Software

Our Tools

Check out our custom software and web-based data tools

         

Compass

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

 

 

Morpheus

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.

manuscript

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

         
         
         
         

LipiDex

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.

LipiDex 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

         
         
         
         

MS-Helios

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

 

Metandem

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

         
         
         
         

LipidGenie

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.

Get the Software

         

         


         

         

Software We Love

Check out some of our favorites

         

MaxQuant

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

manuscript         Get the Software

Perseus

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

manuscript        Get the Software

         
         
         
         
         

OMSSA

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

         
         
         
         
         

D3

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

Enichr

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

manuscript        Get the Software

         

Contact

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.

Contact

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.


Where we are

425 Henry Mall, Coon Lab 4462, Madison WI

777 Highland Avenue, Li Lab 5234, Madison, WI

330 N. Orchard Street, Pagliarini Lab 2268, Madison WI

 

How to contact us

Email address: laura.vantoll@wisc.edu